Re: NADH topology file

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Jul 15 2014 - 09:44:10 CDT

If you open the file toppar_all27_na_nad_ppi.str in a text editor, what do
the first few (~10) lines say?

Additionally, be advised there exists a CHARMM36 force field that has
significant improvements. It can be downloaded with one click at:
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

On 07/15/2014 06:41 AM, Kevin C Chan wrote:
> 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
> Kevin

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