Generate psf file in x-plor format

From: Nehad Elsalamouny (
Date: Thu Nov 17 2016 - 06:07:39 CST

Dear NAMD users,

I want to prepare my protein for NAMD in amber format. I generated a psf file for the protein using amber ff (topology file used is parm14sb_all.rtf) using the following script:

package require psfgen
topology parm14sb_all.rtf
pdbalias residue HIS HIP
pdbalias atom ILE CD1 CD
segment A {pdb xxxxp.pdb}
patch DISU A:42 A:58
patch DISU A:50 A:111
patch DISU A:136 A:201
patch DISU A:168 A:182
patch DISU A:191 A:220
coordpdb xxxxp.pdb A
writepdb xxxx.pdb
writepsf xxxx.psf

When I try to solvate the protein:

package require solvate
solvate xxxx.psf xxxx.pdb -t 5 -o xxxx-wb

I get an error message: unable to open psf file. File is in charmm format should be in x-plor.

However I can see the file is in x-plor format!

Can you help me solve this problem please?



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