Hi all,
I am trying to run amber from phenix with a standard pdb file, no
co-factors etc and struggle already at the phenix.AmberPrep script.
For unknown reasons, the .prmtop file stays empty (0 bytes). I have
tried to figure out from the amber python scripts, where the problem
might be, but didn't find anything obvious (the "self.ns_names" variable
stays empty)
The leap log files states two problems:
1) ......Nonterminal, was not found in name map. (for every single amino
acid)
2) FATAL: Atom .R
On Tue, Jul 12, 2016 at 12:39 PM, R. Gasper-Schönenbrücher < [email protected]> wrote:
Hi all,
I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script. For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty)
The leap log files states two problems: 1) ......Nonterminal, was not found in name map. (for every single amino acid) 2) FATAL: Atom .R
.A does not have a type. (for every single atom) which ends up in: "Failed to generate parameters Parameter file was not saved." There is no .map2 file generated.
Phenix version: dev-2463 Amber: Ambertools 16
Hi, AmberTools16 has renamed the forcefields (for example, leaprc.ff14SB is renamed to leaprc.protein.ff14SB). Please see http://ambermd.org/doc12/Amber16.pdf (page 33, Molecular mechanics force fields) for further info. It's likely that AmberPrep has not updated yet. Hai
Every help is highly appreciated. Many thanks! Best, Raphael
-- Raphael Gasper-Schönenbrücher Universität Bochum AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316 Universitätsstraße 150 44801 Bochum Germany Tel: +49 (0)234-32 27086 Fax: +49 (0)234-32 14762
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Raphael
Hai is correct about Phenix not supporting AmberTools16. I have been
testing the code to support it and plan on releasing it in a short time
frame. I suggest you install AmberTools15 for use with Phenix or wait until
the code is updated.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Jul 12, 2016 at 10:01 AM, Hai Nguyen
On Tue, Jul 12, 2016 at 12:39 PM, R. Gasper-Schönenbrücher < [email protected]> wrote:
Hi all,
I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script. For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty)
The leap log files states two problems: 1) ......Nonterminal, was not found in name map. (for every single amino acid) 2) FATAL: Atom .R
.A does not have a type. (for every single atom) which ends up in: "Failed to generate parameters Parameter file was not saved." There is no .map2 file generated.
Phenix version: dev-2463 Amber: Ambertools 16
Hi,
AmberTools16 has renamed the forcefields (for example, leaprc.ff14SB is renamed to leaprc.protein.ff14SB). Please see http://ambermd.org/doc12/Amber16.pdf (page 33, Molecular mechanics force fields) for further info.
It's likely that AmberPrep has not updated yet.
Hai
Every help is highly appreciated. Many thanks! Best, Raphael
-- Raphael Gasper-Schönenbrücher Universität Bochum AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316 Universitätsstraße 150 44801 Bochum Germany Tel: +49 (0)234-32 27086 Fax: +49 (0)234-32 14762
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
participants (3)
-
Hai Nguyen -
Nigel Moriarty -
R. Gasper-Schönenbrücher