From: Nehad Elsalamouny (nehade_at_uow.edu.au)
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
guesscoord
writepdb xxxx.pdb
writepsf xxxx.psf
exit
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?
Thanks,
Nehad
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