VMD-L Mailing List

From: zeynab hoseyni (zmhoseyni_at_gmail.com)
Date: Sun Feb 28 2016 - 11:16:58 CST

Dear all,

I have a carbon nanotube pdb file and I created the related psf file like
following:
After loading the pdb file in vmd I tried following:
set sel [atomselect top all]
$sel writepdb semi-conductor_cnt.pdb
$sel writepsf semi-conductor_cnt.psf

This procedure goes ahead with no error, but then when I try to solvate
the nano-tube, like following:
package require solvate
solvate semi-conductor_cnt.psf semi-conductor_cnt.pdb -t 10 -o
semi-cond-solv

I received this error:
Info) generating solute plus one replica of water...
psfgen) reading structure from psf file semi-conductor_cnt.psf
psfgen) error reading atoms from psf file

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

When I looked into the error written in the vmd environment I see this
error:
PSF file is in CHARMM format; XPLOR format required.
I thought when I use writepsf command it makes the psf file in the xplor
format but seems I was wrong..

Can anybody help on this?
Thanks,
Zeynab