Re: psfgen question

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 30 2004 - 10:13:35 CST

Hello Minsoo,

Did you get your previous question answered regarding the rna?
If not I think the same problem would explain the current situtation.

Check you pdb file format and make sure it has the standard spacing
between columns.

Brian

On Fri, 30 Jan 2004, MinSoo Kim wrote:

> hi
>
> i'm having trouble with creating a segment for my counter ions...
> this is what i have
> % alias residue NA SOD
> aliasing residue NA to SOD
> % segment SOD {
> auto none
> pdb /Users/visitor2/NAMD/Sodium.pdb
> }
> building segment SOD
> disabling angle autogeneration
> disabling dihedral autogeneration
> reading residues from pdb file /Users/visitor2/NAMD/Sodium.pdb
> extracted 0 residues from pdb file
> Info: generating structure...
> Info: segment complete.
>
> it fails to extract any residue..
> does anyone know why?
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
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