From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Jul 16 2014 - 01:51:22 CDT
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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