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.
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.
Regards
Mustafa
On Fri, Jul 8, 2011 at 5:02 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Mustafa,
>
> On 7/7/2011, at 7:37 a.m., MUSTAFA BUGHIO wrote:
>
> > My job is crashed every time i run sander i dont know how can i over come
> > this problem.
> >
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > In the VDWAALS i guess there is some prblem. The no of residue in my PDB
> > file are 1545. Does this cause any problem in runnig sander?
> > BOND = 1465.5323 ANGLE = 5076.3024 DIHED =
> 14472.5720
> > VDWAALS = ************* EEL = -549369.0011 HBOND =
> > 0.0000
> > 1-4 VDW = 89309.3369 1-4 EEL = 71549.2051 RESTRAINT =
> > 0.2644
> > EAMBER = *************
> >
> > Reply plz
>
> What exactly are you trying to run? If you're trying to do MD, it appears
> as
> though you haven't minimised your system first, and you have pairs of atoms
> that
> are too close to each other. Running an energy minimisation before starting
> MD
> is essential.
>
> If this is not your difficulty, please post your mdin file so we can see
> what it
> is you're trying to do.
>
> 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 - 01:30:03 PDT
