Thanks Ben
I have just been little successful in running minimization f previously
erroneous pentamer by changing min.in parameters. It has worked and have
generated min1.rst which i have used for 2nd minimization in unrestrained.
Thanks again for your guidance.
Regards
Mustafa
On Mon, Jul 11, 2011 at 8:24 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Mustafa,
>
> On 8/07/2011, at 10:50 AM, MUSTAFA BUGHIO wrote:
>
> > Dear Ben i would like to add more that this pentamer protein is membrane
> > protein not soluble one so would you suggest me which forcefield is best
> in
> > this case i m using currently ff99SB.
>
> ff99SB should be fine for proteins.
>
> > And for membrane protein is it possible to get reliable results when
> protein
> > is present in hydrated environment given for MD simulation.Usually people
> > use POPC or DMPC lipid bilayer.
>
> Well, of course if you take a membrane-bound protein and put it in solution
> it's going to behave a bit differently. I'm no expert on bilayer
> simulations
> as opposed to simulations in aqueous solutions, though. Others may be able
> to
> offer more knowledgeable comment.
>
> >
> > Regards
> >
> > Mustafa
> >
> > On Fri, Jul 8, 2011 at 11:29 PM, MUSTAFA BUGHIO <mustafab4.gmail.com>
> wrote:
> >
> >> Thanks Ben
> >>
> >> below is my input file
> >>
> >> Minimization Amber9
> >> &cntrl
> >> imin=1, maxcyc=10000,
> >> ntpr=5, ntr=1,
> >> &end
> >> Restraints
> >> 25.0
> >> RES 1 1545
> >> END
> >> END
> >>
> >> Yes i have checked the pentamers dont superimpose but they are solvated
> in
> >> water box. For confirmation i again opened it in chimera its in pentamer
> >> form. While opening solvated pdb saved from a.promtop and a.inpcrd files
> i
> >> get following error in consol
> >>
> >> warning: duplicate atom serial number found: 69950
> >>
> >> Do this error have any relevance with previous error.
>
> Maybe, but probably not. Duplicate atom numbers are annoying for
> bookkeeping
> purposes, but shouldn't cause the simulation to blow up. Duplicate atom
> positions,
> on the other hand, are very likely to do precisely that. Have you made sure
> that
> no two atoms share the same coordinates?
>
> Also, how many steps of steepest-descent minimisation are you starting off
> with?
> Going directly into conjugate-gradient minimisation is generally considered
> a bad
> idea, because CG doesn't tolerate extremely unfavourable states well, at
> least
> as implemented in Amber. I would suggest running at least 100, and probably
> more
> like 500, steps of steepest-descent minimisation before switching to
> conjugate
> gradients. Please refer to the manual for instructions on how to do that.
>
> Regards,
> Ben
>
> --
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--
MUSTAFA BUGHIO
Junior Research Fellow
Lab # P-133
Computational Medicinal Chemistry and Drug Design
Panjwani Center For Molecular Medicine and Drug Research, International
Center for Chemical Sciences, University of Karachi, Karachi 75270
Pakistan, +923313425010
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Received on Mon Jul 11 2011 - 11:30:03 PDT
