From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu May 08 2014 - 15:57:52 CDT
I don't see any "RESI RET" entry in the retinal topology file (nor in
CGenFF) of the official CHARMM FF. RTAL, yes, but RET, no.
Also, please use the CHARMM36 force field; it has important improvements.
On 05/08/2014 04:11 PM, Faezeh Mottaghitalab wrote:
> Hello everyone
>
> I’m working on bacteriorhodopsin system.
>
> The problem I have is the retinal molecule that is a part of
> bacteriorhodopsin protein.
>
> I download the topology and the parameter file for the retinal from the
> NAMD site. But when I want to make the psf structure the vmd tells that :
>
> psfgen) building segment U
>
> psfgen) reading residues from pdb file 1fbb.pdb
>
> psfgen) unknown residue type RET
>
> psfgen) extracted 225 residues from pdb file
>
> psfgen) Info: generating structure...psfgen) unknown residue type RET
>
> failed!
>
> ERROR: failed on end of segment
>
> MOLECULE DESTROYED BY FATAL ERROR!Use resetpsf to start over.
>
> the question I have is that how can I merge the retinal topology file and
> top_all27_protein_lipid.inp in order to make a correct psf file of whole
> protein with retinal.
>
> The commands I use is:
>
> set 1fbb [atomselect top “all”]
>
> $1fbb writepdb 1fbb.pdb
>
> package require psfgen
>
> topology top_all27_prot_lipid.inp
>
> topology top_ret.inp
>
> pdbalias residue HIS HSE
>
> segment U {pdb 1fbb.pdb}
>
> coordpdb 1fbb.pdb U
>
> guesscoord
>
> writepdb fbb.pdb
>
> writepsf fbb.psf
>
> I really appreciate any help because I’m tired of trying over and over
> without any good result!
>
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