RE: Autopsf error with a modified top file

From: CHINDEA Vlad (
Date: Thu Feb 19 2009 - 18:15:45 CST

Hi Peter


I got the following messages in the VMD console from the initiation of the Autopsf till the crash:


pfrag: 0 ofrag: 0 allfrag: 1 osel: nfrag: 0
Opened coordinate file xxx fo writing
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
Opened coordinate file xxx fo writing
Segment 1: Starting with resid 0, file xxx.pdb
Finished with coordinate file xxx-temp.pdb
Finished with coordinate file xxx-temp.xbgf
Then sometimes when I retry to make the psf again after reset, I got additionally the following messages


"reading topology file"


Then the topology file header with the following errors:


ERROR ! Failed to parse improper statement
ERROR ! Failed to parse CMAP statement
ERROR ! Failed to parse internal coordinate statement

Then a bunch of atom types aliasing and

building segment 01
reading residues from pdb file xxx-temp.pdb
unknown residue type
extracted 1 residue from pdb file
setting patch for first residue to NONE
setting patch for last residue to NONE
Info> generatting structure..
unknown reside type
I would like to mention that the PDB I am using is generated by Facio, a front-end to PC Gamess, after an Optimize QM run and it contains only the HETATM and CONECT records. Also the IMPR, CMAP and IC are not defined in my topology file and although I have the DEFA FIRS NONE LAST NONE in the Top file, Autopsf error message mentions something about the OT2 atome type that I do not have in the molecule and which should belong to a C-terminus carboxyl !


Kind regards to all and many thanks


> Date: Wed, 18 Feb 2009 15:24:59 -0600
> From:
> To:
> CC:
> Subject: Re: namd-l: Autopsf error with a modified top file
> Hi Vlad,
> could you send me the last few lines of output in your console? Usually
> whatever error was encountered will be clearer based on that.
> Best,
> Peter
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