Re: Autopsf error with a modified top file

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 19 2009 - 19:52:52 CST

Hi Vlad,
your topology file actually includes *empty* IMPR, CMAP, and IC
statements, which is syntatically invalid. Try deleting them and see if
things work.
Best,
Peter

CHINDEA Vlad wrote:
> Hi Peter
>
> I got the following messages in the VMD console from the initiation of
> the Autopsf till the crash:
>
> "
> WORKING ON:0
> 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 xxx-temp.top"
>
> 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
> Vlad
>
> > Date: Wed, 18 Feb 2009 15:24:59 -0600
> > From: petefred_at_ks.uiuc.edu
> > To: vchindea_at_hotmail.com
> > CC: namd-l_at_ks.uiuc.edu
> > 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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