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.
Regards
On Fri, Jul 8, 2011 at 8:44 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Mustafa,
>
> On 8/07/2011, at 4:02 AM, MUSTAFA BUGHIO wrote:
>
> > Thanks beb
> >
> > I am new user of AMBER, i have given input file named min500res.in for
> > minimization of my protein. Its pentamer homology model which i have
> > neutralised by adding charges and solvated in TIP3PBOX 10A. Yes you are
> > right that it should be minimized before MD run that's what i am trying
> to
> > do but following error is reported.
> >
> > Other than AMBER minimization i tried to minimize via Sybyl and Modeller
> > optimization program. I found that after minimization my proteins Beta
> > sheets were completely disappeared and formed all loops. But when i
> > minimized only Monomer by same input file it had removed bad clashes and
> my
> > PDB was better refined therefore i am trying to repeat same procedure
> with
> > pentamer which gives VDWAALS error.
>
> I trust that you've ensured your monomers (in the pentamer) aren't
> superimposed.
>
> > Is there any process to minimize VDW forces other than AMBER. If giving
> > cutoff value can help me. as i have not given any cutoff in my input
> file.
>
> Please provide your input file. The cutoff is probably not an issue in this
> case.
> A default value for the cutoff will be used if it's not explicitly set.
>
> 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 Fri Jul 08 2011 - 08:00:05 PDT
