VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jun 09 2003 - 09:33:06 CDT

Hi,

You need to move "alias residue ..." before "segment A2P ..." in the
script. Residue aliases are used at segment creation, while atom aliases
are not used until coordinates are read in.

-Jim

On Mon, 9 Jun 2003, Dr. Daniel James White PhD wrote:

> Hi all,
>
> I'm trying to use psfgen to make psf and pdb files required for NAMD
> input for my protein
>
> I get an error saying unknown residue type HIS,
> but I have make an alias in the script so HIS is understood as HSE
> "alias residue HIS HSE"
> but It isn't working,
>
> what am I doing wrong? see psfgen script and output below
>
> cheers
>
> Dan
>
>
>
> ----- begin script------
> topology top_all27_prot_na.inp
>
> segment A2P {
> pdb output/a2prot.pdb
> }
>
> patch DISU a2protein:102 a2protein:120
> patch DISU a2protein:64 a2protein:53
> patch DISU a2protein:836 a2protein:847
> alias residue HIS HSE
> alias atom ILE CD1 CD
> coordpdb output/a2prot.pdb A2PR
>
> segment MN {
> auto none
> pdb output/a2Mn.pdb
> }
> coordpdb output/a2Mn.pdb MN
>
> writepsf output/a2allfrompsfgen.psf
>
> guesscoord
>
> writepdb output/a2allfrompsfgen.pdb
>
> ENDMOL
> ----end----
>
>
> ------begin output------
> bash-2.05b$ psfgen a2psfgenscript.txt
> PSFGEN from NAMD 2.5b1 for Linux-i686
> reading topology file top_all27_prot_na.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<<
> 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 Nucleic Acid Topology File ////
> \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
> Alexander D. MacKerell Jr. and Nicolas Foloppe
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> duplicate residue key CAL will be ignored
> ERROR! Failed to parse residue statement.
> duplicate residue key DUM will be ignored
> ERROR! Failed to parse residue statement.
> building segment A2P
> reading residues from pdb file output/a2prot.pdb
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> extracted 1128 residues from pdb file
> generating structure at end of segment
> unknown residue type HIS
> ERROR: failed on end of segment
> while executing
> "segment A2P {
> pdb output/a2prot.pdb
> }"
> (file "a2psfgenscript.txt" line 3)
> bash-2.05b$
> ---------end output-------
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box 35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 (0)14 260 4183 (work)
> +358 (0)414740463 (mob)
>
> http://www.chalkie.org.uk
> dan_at_chalkie.org.uk
> white_at_cc.jyu.fi
>