From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Wed May 17 2017 - 15:58:37 CDT
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
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