From: beckloni_at_umdnj.edu
Date: Sun May 09 2004 - 10:00:59 CDT
Greetings,
I am attempting to generate a psf file for two different molecules,
trypsin and a novel analogue. Unfortunately, the pgn file will only read
the C and N terminus of the analogue, not the rest of the molecule. I have
attempted to add the missing residues through such commands as residues and
even alias residues but nothing seems to work. Is there something that I am
doing wrong here?
Here is my pgn file setup:
package require psfgen
topology top_all27_prot_tst.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment TRP {
pdb trp.pdb
}
patch DISU TRP:22 TRP:157
patch DISU TRP:42 TRP:58
patch DISU TRP:128 TRP:232
patch DISU TRP:136 TRP:201
patch DISU TRP:168 TRP:182
patch DISU TRP:191 TRP:220
coordpdb trp.pdb TRP
segment ANA {
pdb analogue.pdb
first CTER
last NTER
}
coordpdb analogue.pdb ANA
guesscoord
writepdb trpd.pdb
writepsf trpd.psf
Both of the segment file formats are out of SPDBV to rebuild the missing
side chains. The analogue file was built as one single chain in Sybyl.
Sincerely,
Nicholas Beckloff
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