about psfgen

From: emilia.l.wu (emilia.l.wu_at_gmail.com)
Date: Sat Jul 04 2009 - 08:59:44 CDT

Hi all,

I use? the psfgen script below to read a pdb file, guess some coordinates for missing atoms and get another pdb and corresponding
psf file. but I notice if I use vmd -psf prod.psf -pdb prod.pdb to see the structure, It is obvious that there is some problem of the bond of
ILE1, some bonds are broken, and if I use vmd -pdb prod.pdb to open it, it looks good. so it should be the problem of the psf file.
cound anyone tell me what 's the problem of the script.

# PSFGEN script to generate PSF from split up PDB file
package require psfgen

topology "top_mod.rtf"

segment PROD {
?first ACE
?last CT2
?pdb m1_prod_ADTaddH.pdb_charmm
}
pdbalias atom ILE CD1 CD
coordpdb m1_prod_ADTaddH.pdb_charmm PROD

guesscoord

patch DISU PROD:2 PROD:12

writepdb prod.pdb
writepsf prod.psf

quit

#ENDMOL

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