Duration of a phenix.elbow run
Hi, I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output: MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4). Any help would be very appreciated Thanks Dirk
Dirk That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was you, I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2 minutes. Nigel On 7/1/09 2:43 PM, Dirk wrote:
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
What I do in these cases is a MM minimization of the ligand using a high quality forcefield and using that output as input into elbow and not perform an optimization, but have it generate the restraints directly from the input. The differences between the forcefield and the AM1 calculation in elbow are negligible for protein crystallography purposes. I would not waste time on o.n. runs. HTH Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nigel W Moriarty Sent: Wednesday, July 01, 2009 7:26 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Duration of a phenix.elbow run
Dirk
That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was you, I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2 minutes.
Nigel
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable
On 7/1/09 2:43 PM, Dirk wrote: phenix
release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
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Hi Carsten,
is there a simple program for a MM minimization of the ligand? The prodrg
server changes atom labels and therefore is not convenient. Do you use sybyl
or what else?
Maia
----- Original Message -----
From: "Schubert, Carsten [PRDUS]"
What I do in these cases is a MM minimization of the ligand using a high quality forcefield and using that output as input into elbow and not perform an optimization, but have it generate the restraints directly from the input. The differences between the forcefield and the AM1 calculation in elbow are negligible for protein crystallography purposes. I would not waste time on o.n. runs.
HTH
Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nigel W Moriarty Sent: Wednesday, July 01, 2009 7:26 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Duration of a phenix.elbow run
Dirk
That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was you, I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2 minutes.
Nigel
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable
On 7/1/09 2:43 PM, Dirk wrote: phenix
release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
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Hi, thanks for the suggestions I tried to run it overnight, but without any result. I also tried to use GAMESS, but even so the GAMESS run is started I still get the message "GAMESS doesn't seem to be installed" and "mv: Aufruf von stat für „elbow.drgfin_pdb.012.gamess.gam“ nicht möglich: No such file or directory" even so the file exists. Since I'm not experienced in python I wasn't able to find the reason for that by inspecting the GAMESSMixins.py script. I would like to try the forcefield approach, but don't know if there is any freeware available for that purpose - I would be glad about suggestions . For the moment I "solved" the problem by manually editing the cif file using values from the refmac monomer and link libraries for the restraints. I still would be really interested in getting elbow to work to get better restraints for this ligand and to avoid the time consuming manual creation of cif files in the future. Thank you again for the replies Dirk Schubert, Carsten [PRDUS] schrieb:
What I do in these cases is a MM minimization of the ligand using a high quality forcefield and using that output as input into elbow and not perform an optimization, but have it generate the restraints directly from the input. The differences between the forcefield and the AM1 calculation in elbow are negligible for protein crystallography purposes. I would not waste time on o.n. runs.
HTH
Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nigel W Moriarty Sent: Wednesday, July 01, 2009 7:26 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Duration of a phenix.elbow run
Dirk
That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was
you,
I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2
minutes.
Nigel
On 7/1/09 2:43 PM, Dirk wrote:
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand
after
refinement. I tried to get an optimized cif by using --opt command,
but
the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization
needs
such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable
phenix
release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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Dirk Lets talk off-line. Can you send me the input that you send to eLBOW? You do need to have GAMESS installed and then you need to do a small bit of scripting by changing the GAMESS.csh file. I can help with that. Nigel On 7/3/09 5:27 PM, Dirk wrote:
Hi,
thanks for the suggestions I tried to run it overnight, but without any result. I also tried to use GAMESS, but even so the GAMESS run is started I still get the message "GAMESS doesn't seem to be installed" and "mv: Aufruf von stat für „elbow.drgfin_pdb.012.gamess.gam“ nicht möglich: No such file or directory" even so the file exists. Since I'm not experienced in python I wasn't able to find the reason for that by inspecting the GAMESSMixins.py script. I would like to try the forcefield approach, but don't know if there is any freeware available for that purpose - I would be glad about suggestions . For the moment I "solved" the problem by manually editing the cif file using values from the refmac monomer and link libraries for the restraints. I still would be really interested in getting elbow to work to get better restraints for this ligand and to avoid the time consuming manual creation of cif files in the future.
Thank you again for the replies
Dirk
Schubert, Carsten [PRDUS] schrieb:
What I do in these cases is a MM minimization of the ligand using a high quality forcefield and using that output as input into elbow and not perform an optimization, but have it generate the restraints directly from the input. The differences between the forcefield and the AM1 calculation in elbow are negligible for protein crystallography purposes. I would not waste time on o.n. runs.
HTH
Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nigel W Moriarty Sent: Wednesday, July 01, 2009 7:26 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Duration of a phenix.elbow run
Dirk
That is quite a large molecule but it shouldn't take a few hours. I'm not sure what is happening but I'd guess that a convergence is failing and the upper limit on the number of steps is too great. If I was
you,
I'd run it overnight and if that fails run it in another quantum package to get the geometry you desire. A different run MAY generate a different starting geometry for the --opt option and that may work better. Each step of the optimisation should take less than 2
minutes.
Nigel
On 7/1/09 2:43 PM, Dirk wrote:
Hi,
I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand
after
refinement. I tried to get an optimized cif by using --opt command,
but
the program just runs up to the following output:
MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size
and then nothing happens for several hours. Does the optimization
needs
such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable
phenix
release (1.3) and the current version (1.4).
Any help would be very appreciated
Thanks
Dirk
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Hi Nigel, I am wondering why phenix cannot use ready cif files for ligands from the PDB. I downloaded an ideal pdb for a ligand (LMT) and tried to use its cif file from the PDB. It did not work. I had to run elbow and produce an elbow.LMT_ideal cif file to make it work. Maia
Hi all, I need to make a cif_link_params file for a covalent ligand bound to a sulfur in one of the alterantive conformations. What is the syntax for such an atom: SG_A or ASG or A_SG etc? Maia
Hi Maia, I might be misunderstanding your question, but can't you define the bond between these atoms using "custom bonds": http://phenix-online.org/documentation/refinement.htm#anch80 ? You can select such atom like this: "chain X and resseq 123 and name YZ and altloc A" You can experiment with atoms selections (to see which exactly atoms you are selecting) using this very handy tool: phenix.pdb_atom_selection model.pdb "your_atom_selection_string" Pavel. On 7/20/09 5:21 PM, Maia Cherney wrote:
Hi all, I need to make a cif_link_params file for a covalent ligand bound to a sulfur in one of the alterantive conformations. What is the syntax for such an atom: SG_A or ASG or A_SG etc?
Maia
Hi Maia,
I need to make a cif_link_params file for a covalent ligand bound to a sulfur in one of the alterantive conformations. What is the syntax for such an atom: SG_A or ASG or A_SG etc?
Sorry, the cif_link mechanism doesn't work for your situation. It is something I hadn't anticipated when writing the link code. I'll put this on my todo list. Could you try custom bonds in this case? -- There are also custom angles if you want those as well. If you could send me the residues from your .pdb file you want to link, I'll have an easier start changing the cif link code to handle your situation. Ralf
participants (7)
-
chern -
Dirk -
Maia Cherney
-
Nigel W Moriarty -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Schubert, Carsten [PRDUS]