Re: RetinalTop

From: Ale Gomez (agomez.fisica_at_epn.edu.ec)
Date: Mon Aug 02 2010 - 11:07:52 CDT

Hi Bjoern and thanks for your help.
In my pdb file (1C3W), retinal's resname is RET and in the repository file
is a resname LYR. I know that retinal is linked with LYS 216 and I do not
sure If I should change it in my pdb file. Should I change just the RET
resname or LYS 216 too?.
I tried change both to LYR and running vmd, and I think works fine. But when
I tried to minimize my system with NAMD I found this messages:
Warning: VDW TYPE NAME CR15 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR14 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR13 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR12 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR11 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR10 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR9 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR8 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR7 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR6 MATCHES PARAMETER TYPE NAME CR*
Warning: VDW TYPE NAME CR5 MATCHES PARAMETER TYPE NAME CR*

It could be a reason that my system became unstable???.
Thanks for your help and sorry about the cross post.

-------------------------------------------------------------------
Ale Gómez
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/

On 2 August 2010 09:49, Bjoern Olausson <namdlist_at_googlemail.com> wrote:

> 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-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>

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