Re: [AMBER] sander job crashed

From: Ben Roberts <ben.roberts.geek.nz>
Date: Mon, 11 Jul 2011 11:24:21 -0400

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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Received on Mon Jul 11 2011 - 08:30:03 PDT
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