VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Mon Jun 09 2003 - 08:48:32 CDT

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