AMBER Archive (2007)

Subject: Re: AMBER: error in running sander

From: devrani mitra (devranimitra_at_gmail.com)
Date: Tue May 29 2007 - 17:01:40 CDT

Hello

Thanks for the reply. Well, I was trying to simulate the Fe protein of
nitrogenase (PDB code 2C8V) following the tutorials provided in AMBER
homepage as I'm new to AMBER. My protein contains Mg-ATP as well as
4Fe-4S cluster. I collected the parameter files for Mg and ATP from
AMBER parameter database but could not generate the parameter file for
Fe-S cluster (for this I had posted my msg barely a week back but did
not get any reply) even though I tried with AMBER parameter
development tutorial. However, I've the values for force constants.
So, I deleted the Fe-S cluster from my pdb and continued with
generating parameter files, co-ordinate files as well as solvating my
structure etc.
Therefore, the root problem in generating the bad structure may be in
connection with deleting the Fe-S cluster from pdb. If I can generate
the parameter file for Fe-S, will it help in avoiding the error msg?

Best,
Devrani

On 5/29/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> if your structure is so bad that the energies aren't even printable
> then you might try minimization in gas phase or perhaps GB before
> adding water. that will just make it even more difficult.
> have you looked at the atoms with GMAX? perhaps you can modify
> them by hand first? Amber is not always graceful at dealing with
> huge energies and very bad structures, especially in solution.
>
> again, it is very hard to help since you haven't told us what you
> are trying to do. making us read your output to see what is there
> will not help you get more people to help you.
>
>
>
> On 5/29/07, devrani mitra <devranimitra_at_gmail.com > wrote:
> > Hello
> >
> > I'm attaching the output file for the details. Hope this simplifies the
> things.
> >
> > Thanks,
> > Devrani
> >
> > On 5/29/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> > > does your a_min_water.out file have any information in it?
> > >
> > > do the test cases pass?
> > >
> > > you need to give us much more information if you want help.
> > >
> > >
> > > On 5/29/07, devrani mitra <devranimitra_at_gmail.com > wrote:
> > > > Dear AMBER users,
> > > >
> > > > While running sander (for removing the bad contacts) following the
> > > > tutorials, I'm getting the following error message:
> > > >
> > > > >> sander -O -i a_min.in -p a.parm7 -c a.crd -r a_min.rst -o
> > > > a_min_water.out -ref a.rst
> > > >
> > > > p0_29153: p4_error: interrupt SIGSEGV: 11
> > > >
> > > > I'm not getting as which file do I need to correct. Please suggest.
> > > >
> > > > Thanks!
> > > > Devrani
> > > >
> > > > Devrani Mitra, UC Davis
> > > >
> > >
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> > >
> >
> >
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>
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