[AMBER] Using Chamber to convert psf to prmtop

From: Frank X. Vázquez <fxv.umich.edu>
Date: Fri, 21 Jan 2011 14:33:04 -0600

Hello Amber users,

I have been to trying to convert a NAMD psf file to an AMBER topology
file and have received the following error:
PGFIO-F-231/formatted read/unit=20/error on data conversion.
  File name = ebar_charmm.psf formatted, sequential access record =
  In source file _psfprm.f, at line number 2177

Using the psfgen plugin in VMD, converted the NAMD psf file to charmm
formt with this script:
topology top_all27_prot_lipid.rtf
readpsf ebar_solv.psf
coordpdb ebar_solv.pdb
writepdb ebar_charmm.pdb
writepsf charmm cmap ebar_charmm.psf

I then ran chamber using
chamber -top top_all27_prot_lipid.rtf -param par_all27_prot_lipid.prm
-psf ebar_charmm.psf -crd ebar_charmm.pdb -p ebar.prmtop -inpcrd
ebar.inpcrd -cmap -verbose

If anyone has any advice or help I would really appreciate it.

Frank X. Vázquez

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Received on Fri Jan 21 2011 - 13:00:02 PST
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