Re: RetinalTop

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 02 2010 - 09:49:32 CDT

On Monday 02 August 2010 15:52:10 Ale Gomez wrote:
> Hi everyone.
> I am trying to simulate bacteriorhodopsin in a lipid membrane but in charmm
> topology there is not topology for retinal. I found this
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?ParameterTopologyReposi
> tory but
> I am not sure how should I use it. I have to just add it into the topology
> file I am using??. Same situation for parameter file.
> Thanks in Advance
> Kind Regards
>

Don't cross post to VMD.

In NAMD you can load the Retinal parameter file additional to your current
parameter file file.

#######################
paraTypeCharmm on
parameters ../par_all27_prot_lipid.prm
parameters ../retinal.prm
#######################

In CHARMM you have to load both par/top file. When loading the Retinal
topology file, take care that the Retianl topology file does not contain any
overlapping MASS values. If it happens to have overlapping MASS entries,
change them but then you have to regenerate your PSF to reflects the changed
MASS entries. So merge the retinal top/par files with your current top/par
files and change the MASS entries for Retinal not to contain duplicates.

Read more in the CHARMM-Forum about this topic:
http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24193#Post24193

Cheers
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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