My problem seems to be not the pdb file but the handshaking between phenix and amber. If works with the sbgrid installation, so I will just use that. Thanks for the help, G

On Dec 24, 2025, at 14:01, James Holton wrote:

Well, what does leap.log look like?

Also, I don't see an attachment from here.

On 12/24/2025 10:05 AM, George Phillips wrote:

...

I am trying to run phenix.AmberPrep in phenix-2.0-5885 and get the flollowing but cannot find a leap.log file to check. Any clues? pdb file attached. Thanks, George georgep@Y56NQ4XRRC 7W26 % phenix.AmberPrep noH.pdb minimise=amber_all ================================================================================ Running pdb4amber on noH.pdb ================================================================================

================================================== Summary of pdb4amber for: noH.pdb ===================================================

----------Chains The following (original) chains have been found: A B S

---------- Alternate Locations (Original Residues!))

The following residues had alternate locations: None -----------Non-standard-resnames

---------- Missing heavy atom(s)

None ================================================================================ Setting up library files for non-standard residues ================================================================================ ================================================================================ Preparing asu files and 4phenix_noH.pdb ================================================================================ Checking output filenames file : noH_asu.prmtop Sorry: Output file not present : noH_asu.prmtop Check contents of “leap.log"

 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s