problem reading topolgy files

From: Annalisa Marsico (annalisa.marsico_at_biotec.tu-dresden.de)
Date: Sun Dec 10 2006 - 06:14:51 CST

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Hi all,
I am trying to create a psf file for the Rhodopsin dimer with retinal
and palmytolated cysteins
When I try to run my script generate_psf.tcl I have some problem reading
the topology file top_all27_prot_lipid.inp.
The error that I get is the following:

SFGEN from NAMD 2.6b1 for Linux-i686
reading topology file
/home/bioinf/annalisa/Rhodopsin_simul_new/top_all27_prot_lipid.inp

>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
from
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
and
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr. email: alex,mmiris.ab.umd.edu
              telephone: 410-706-7442

Created by CHARMM version 27 1
ERROR! Explicit exclustions not supported, atom ignored.
ERROR! Explicit exclustions not supported, atom ignored.

When I try to read the topology file PalmytolCys_top.inp (download from
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?ParameterTopologyRepository
) the error I get is the following:

PSFGEN from NAMD 2.6b1 for Linux-i686
reading topology file
/home/bioinf/annalisa/Rhodopsin_simul_new/PalmytolCys_top.inp

ERROR! Unusual CHARMM version record.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
no residue in progress for atom
ERROR! Failed to parse atom statement.
ERROR! Explicit exclustions not supported, atom ignored.
ERROR! Explicit exclustions not supported, atom ignored.

etc...

I don't understand if I use the wrong topology files or the wrong
version of NAMD..

Thanks in advance for any help!

Annalisa

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