NADH topology file

From: Kevin C Chan (
Date: Tue Jul 15 2014 - 05:41:51 CDT

Hi NAMD forum,

        Does any one has successfully built psf file for NADH? I was
using stream file (toppar_all27_na_nad_ppi.str) to build a psf file for
NADH but it simply fails by giving:

> building segment A
> reading residues from pdb file m.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> unknown atom type HN1
> add atom failed in residue NAD:1
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

The atoms name in my pdb file (non hydrogen atoms) are same as in
*toppar_all27_na_nad_ppi.str* file.

Also attached is my psfgen.pgn, in which I have copy&paste NADH part of
*toppar_all27_na_nad_ppi.str* into *ppi_top.inp* and add an "*END*" to it:

> package require psfgen
> resetpsf
> topology ppi_top.inp
> segment NADH {
> auto none
> pdb NADH.pdb
> }
> coordpdb NADH.pdb NADH
> guesscoord
> writepsf nadh.psf
> writepdb nadh.pdb

Actually I have tried replace the topology command for psfgen as

topology top_all27_na_nad.rtf
> topology ppi_top.inp

and amazingly solve the problem above however I will get a nonsense psf and
pdb files with coordinates missing. So it does not work neither.

If anyone has experience on this, I will appreciate any advice.

Thank you

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