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.
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.
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.
>
> 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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>>
>>
>>
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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
>
>
--
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 - 08:00:06 PDT
