From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed May 17 2017 - 16:12:41 CDT
Hi Sadegh,
There is a non-psfgen way of doing this. Take a look at topotools (http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/), specifically the mergemols command in the utility functions. Also, is this a XPLOR formatted psf? I see numbers in an atomtype column, which makes me think this was made in CHARMM. I'm not sure how NAMD will handle this now, but in the past, this wouldn't simulate regardless.
-Josh
On 05/17/2017 03:03 PM, Sadegh Faramarzi Ganjabad wrote:
Dear NAMD users,
I have two sets of psf/pdb files for a protein and a solvent and want to merge them with VMD with the following simple script
package require psfgen
readpsf protein.psf
readpsf water.psf
coordpdb protein.pdb
coordpdb water.pdb
writepsf all.psf
writepdb all.pdb
both psf files can be read with VMD. However, when I put 'readpsf water.psf' it gives the following error
psfgen) reading structure from psf file water.psf
psfgen) error reading atoms from psf file
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
I am not sure what is wrong with 'water.psf', because it has the same format as 'protein.psf". Here is the beginning of the file
PSF
1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file
23592 !NATOM
1 WT 1 TIP3 OH2 3 -0.834000 15.9994 0
2 WT 1 TIP3 H1 1 0.417000 1.0080 0
3 WT 1 TIP3 H2 1 0.417000 1.0080 0
4 WT 2 TIP3 OH2 3 -0.834000 15.9994 0
5 WT 2 TIP3 H1 1 0.417000 1.0080 0
6 WT 2 TIP3 H2 1 0.417000 1.0080 0
7 WT 3 TIP3 OH2 3 -0.834000 15.9994 0
******************************************************************************
Am I doing something wrong?
Thanks,
Sadegh
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:18 CST