VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jan 17 2007 - 05:49:13 CST

Hi,

** Please disregard my previous email, it was sent by mistake **

I am trying to read a multi-segment pdb/psf pair, do a few things, and
write out a new pair. However, the new psf that vmd writes has atomnames
in both the 5th and 6th column, instead of the atom types in the 6th
columns. This probably means that I am not reading the psf correctly, and
the atom types are not being assigned. Can someone please point to my
mistake ? Here is what I am trying to do:

########
mol delete all
resetpsf
topology top_all27_prot_lipid.inp

# READ A MULTI-SEGMENT PSF
readpsf prot-water.psf
coordpdb prot-water.pdb
mol load pdb prot-water.pdb

# BLAH BLAH

# WRITE OUT
set all [atomselect top all]
$all writepdb out.pdb
$all writepsf out.psf

Thank you,

-Himanshu