Re: psfGen error

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Tue Nov 20 2007 - 09:17:00 CST

Hi Joseph,
    I would check the formating of your PDB file. When I looked at it
under another program, the columns were not aligned. The format of the
PDB file is very precise, everything must be in the right column and
you can't have any <TAB> characters separating entries. Entiries must
be separated by <spaces>.

Regards,
    Jeff

Joseph Heil wrote:

> I am using the psfgen NAMD extension in VMD to try and generate a psf
> file for ammonia. I get the error: Warning: failed to set coordinate
> for atom 1H MOL:1 U
> same problem for the other 2 hyrdogens but not for nitrogen
> so I think the error is in my pdb file.
> pdb file:
> ! 1 2 3
> 4 5 6 7
> !2345678901234567890123456789012345678901234567890123456789012345678901234567890
> ATOM 1 N MOL U 1 0.000
> 0.000 0.000 1.00 0.00
> N
> ATOM 2 1H MOL U 1 -0.000
> 0.363 1.028 1.00 0.00 H
> ATOM 3 2H MOL U 1 -0.890
> 0.363 -0.514 1.00 0.00 H
> ATOM 4 3H MOL U 1 0.890
> 0.363 -0.514 1.00 0.00 H
> END
>
> topology file:
>
> ! 1 2 3 4
> !23456789012345689012345678901234567890
> MASS 1 N1 14.01 N
> MASS 2 H1 01.008 H
> !DEFA FIRS NTER LAST CTER
> !AUTO ANGLES DIHE
> ! 1 2 3 4
> !23456789012345689012345678901234567890
> RESI MOL 0.00
> GROUP
> ATOM N N1 -.600
> ATOM 1H H1 +0.200
> ATOM 2H H1 +0.200
> ATOM 3H H1 +0.200
> BOND N 1H N 2H N 3H
> DEFA FIRS NTER LAST CTER
> AUTO ANGLES DIHE
> PATCHING FIRS NONE LAST NONE
>
> any suggestions on what to change or knowledge on space dependent
> formatting of topology files would be greatly appreciated.
>
> Thank you,
>
> Joseph Heil
> NC State University
> College of Textiles
> Textile Engineering Chemistry and Science

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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