do you get the bad energies when you don't include the Fe-S or Mg-ATP atoms?
On 5/29/07, devrani mitra <devranimitra.gmail.com> wrote:
>
> 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.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.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.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.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
> > > > >
> > > >
> > -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
> > > > > To post, send mail to amber.scripps.edu
> > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed May 30 2007 - 06:07:31 PDT
