Hi,
I have a question regarding the implementation of nonstandard residues in
AMBER. Having crafted such a residue, I am attempting to use that residue to
load a pdb file containing two proteins, one of which has a single instance
of the nonstandard residue. (In the process, I have used Gaussian03,
antechamber, parmchk to obtain a *.lib file of the residue and a *.frcmod
file containing the missing parameters to be loaded into XLEaP). After
loading the library file and frcmod file I created, XLEaP successfully loads
the pdb file with no error messages. However, when, I attempt to generate
Amber parameters using the command,
saveamberparm proteins proteins_vac.prmtop proteins_vac.inpcrd,
I get the following error messages and the parameters aren't saved:
***********************************************************
Checking Unit.
Buliding topology.
Building atom parameters.
Building bond parameters
Could not find bond parameter for : C - NT
Building angle parameters.
Could not find angle parameters: O - C - NT
Could not find angle parameters: C - NT - CT
Could not find angle parameters: C - NT - H
Could not find angle parameters: CT - C - NT
Could not find angle parameters: C - CT - NT
Building proper torsion parameters
** No torsion terms for O-C-NT-CT
** No torsion terms for O-C-NT-H
** No torsion terms for CT-C-NT-CT
** No torsion terms for CT-C-NT-H
Building improper torsion parameters.
total 356 improper torsions applied.
Building H-Bond parameters.
Parameter file was not saved.
***********************************************************
I would like to first understand some background on this error and would be
grateful for any suggestions working towards solving it.
Some troubleshooting I have already tried:
1) Use reduce -Trim command on the pdb file
2) View the frcmod file (which should contain any missing parameters) and
identify any "ATTN needs revision" flags (Three exist in the file, but have
no correlation to the error messages above)
Thanks,
Darren Jindal
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 12 2011 - 20:00:02 PDT
