Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90)

From: Jason Swails <>
Date: Thu, 14 Aug 2014 13:37:46 -0400

On Thu, 2014-08-14 at 17:09 +0000, Sarah Witzke wrote:
> D'oh!
> No I didn't - but I did now, and then I get an error about a wrong PSF molecule section:
> > chamber -top top_all36_lipid.rtf -top top_all36_cgenff.rtf -param par_all36_lipid.prm -param par_all36_cgenff.prm -str toppar_all36_lipid_cholesterol.str -str toppar_water_ions.str -psf step5_assembly.psf -crd step5_assembly.pdb -box 72.5,72.5,82 -nocmap
> Creating chamber topology file from PSF step5_assembly.psf, RTF files [top_all36_lipid.rtf, top_all36_cgenff.rtf], PAR files [par_all36_lipid.prm, par_all36_cgenff.prm], and STR files [toppar_all36_lipid_cholesterol.str, toppar_water_ions.str]. Coords from step5_assembly.pdb. NO CMAP. Box info [72.5, 72.5, 82.0, 90.0, 90.0, 90.0]. GB Radius set mbondi.
> CharmmPSFWarning: Detected PSF molecule section that is WRONG. Resetting molecularity.

This is just a warning. It's a known problem with CHARMM-GUI (the MOLNT
section is filled out with a bunch of 1's, which is wrong).

> AmberParmWarning: POINTERS flag not found! Likely a bad AMBER topology file.

Haven't seen this one before... Can you send me the files I need to
reproduce this problem off-list?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Aug 14 2014 - 11:00:02 PDT
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