AMBER Archive (2008)

Subject: Re: AMBER: ptraj has trouble with x-plor psf file from VMD

From: Jufang Shan (jufang.shan_at_gmail.com)
Date: Mon Jun 02 2008 - 10:52:28 CDT

Hi Dong,

I am not sure whether the residue number in your psf/dcd starts from 1 or
not. If not, ptraj will change it to 1, I think.

Best,
Jufang

On Thu, May 29, 2008 at 4:23 PM, Dong Xu <d1xu_at_ucsd.edu> wrote:

> Hi All,
>
> I'm having problem with ptraj processing x-plor psf file generated
> from VMD. The ouput looks like:
>
> ********************************************************************
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "Cheatham lab development full version 9.9h" (4 April 2008)
> -/- Executable is: "ptraj"
> /-\
> \-/ Reading in CHARMM PSF file
> Reading in the title...
>
> REMARKS VMD generated structure x-plor psf file
>
> Total number is atoms is 7614
> Reading in the atom information...
> Dumping out residue names:
> N N C1 C1 C2
> Dumping state information...
> atoms: 7614
> residues: 5
> box length: 0.000 0.000 0.000
> box angles: 90.000 90.000 90.000
> molecules: 487
> max frames: 0
>
> PTRAJ: rms first out rms_fit21stpsf.txt :110-262_at_CA,C,N,O
> Mask [:110-262_at_CA,C,N,O] represents 0 atoms !!!NO ATOMS DETECTED!!!
> [No output trajectory specified (trajout)]
> ********************************************************************
>
> Obviously the residue names are read incorrectly and mask selection is
> not accepted either. Is this caused by the difference between x-plor
> psf file and CHARMM psf file?
> Reading DCD trajectory file works fine and pdb/dcd combination also works.
>
> Thanks,
>
> Dong Xu
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