Re: Re: NADH topology file

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Jul 16 2014 - 12:39:02 CDT

I'm sorry, I didn't look that far down your e-mail; most people don't
start an e-mail with an error message only to mention further down they
got around that error and actually want help with a *different* issue.

I don't know why you get "a nonsense psf" but I can assure you not reading
all the required files won't solve anything. Among other things, NADH
contains the atom type NH1, which is defined in the main nucleic acid file...

CHARMM36 would be worth giving a try; there's a very small chance that the
modularization of the force field somehow prevents triggering your issue.

On 07/16/2014 02:51 AM, Kevin C Chan wrote:
> ​Thank you Kenno
>
> ​I have looked at the stream file and know that it requires parent files
> to be read first.
> As I have mentioned that I have tried
> /
> ​
> > topology top_all27_na_nad.rtf
> //> topology ppi_top.inp /
> and it gives very weird ​psf and pdb files in which some coordinates are
> missing and strange bonds are connected. Is this a correct way to "read
> parent files prior to streaming the stream file"?
>
> ​I have downloaded the newest force-field but for some reason I am using
> the older one. I will turn back to CHARMM36 soon. Thank you anyway.​
>
> ​Regards,
> ​Kevin​
> ​
>
> 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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