On Thu, Jan 10, 2013 at 4:06 PM, Date, Mihir <Mihir.Date.stjude.org> wrote:
> Thanks,
> I did replace readmd.F90 with new readmd.F90 (having F atom radius) and
> rebuild Amber 12 again. ( while configuring it, I let Amber12 update
> patches though. Would it hurt?)
>
If there is no error message, then you will probably be fine. Looking at
the available bug fixes, there is nothing that should conflict with the
changes you are adding. So yes, it is fine to update.
> I can run GB calculation without problem but PB crashes for MMPBSA.py.MPI.
> Also I still can't run decomposition per residue calculations.
> Attached are out put files.
> One is the output of PB (mmpbsa_py.clean.out) and core dump
> (mmpbsa_py.stacktrace.out) when it crashed. It did created _MMPBSA_* files
> though and core.*
>
> Another is output of decomposition calculation (decomp.clean.out).
>
>
> Any help/suggestions are highly appreciated.
> Regards,
>
> Mihir
> ________________________________________
> From: Vaibhav Dixit [vaibhavadixit.gmail.com]
> Sent: Friday, January 04, 2013 10:16 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] bad atom type: f. .
>
> Hi,
> I had faced such error with F and Cl atoms earlier.
> For this I replaced the file "readmd.f90" in the $AMBERHOME/src/sander/
> folder with the one attached while recompling the sander using following
> steps.
> I hope this helps.
>
> Steps
>
> 1. Extract the source
> 2. set the AMBERHOME
> 3. /patch_amber.py --update-tree
> 4. replace the readmd.f90 file
> 5. Configure without update -- ./configure --no-updates gnu
> 6. make
> 7. make install
> 8. make test
>
> For details on how to make the changes to the mdread.f90 file you can refer
> this page http://archive.ambermd.org/201101/0220.html
>
> On Sat, Jan 5, 2013 at 12:12 AM, Date, Mihir <Mihir.Date.stjude.org>
> wrote:
>
> > Dear Amber users,
> > My ligand in protein-ligand complex contains 6 fluorines. I am running
> > MMPBSA calculations with Amber 12 for protein-ligand binding free energy.
> > When I run only MM-PB/GB-SA, it runs fine. But only when I want to
> > decompose energy on per residue basis using &decomp namelist, it crashes
> > with message
> >
> > bad atom type: f
> > CalcError: /ibis/bashford/amber12/bin/sander failed with prmtop
> > complex.prmtop!
> >
> > If I am to suspect complex.prmtop, then it should have given the same
> > error for MM-PB/GB-SA calculations, but it does not.
> > I did read messages on archive about this same error. Do I need to patch
> > the parameters of Fluorine on Amber 12?
> >
> > Here are my inputs for
> >
> > &general
> > endframe=8000, interval=1000, keep_files=2,
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100,
> > /
> > &decomp
> > idecomp=1, print_res="2-274; 277-549"
> > dec_verbose=2,
> > /
> >
> > MMPBSA.py -O -i mmpbsa-1.in -o MMPBSA.dat -do MMPBSA_DECOMP.dat -sp
> > complex-tip3.prmtop -cp complex.prmtop -rp DH61-ab.prmtop -lp lig.prmtop
> -y
> > prod-NVT-8ns.mdcrd prod-NVT-16ns.mdcrd
> >
> > I am using interval 1000 for test run to make calculation quicker.
> >
> > Any appreciate help/suggestions.
> >
> > Email Disclaimer: www.stjude.org/emaildisclaimer
> > Consultation Disclaimer: www.stjude.org/consultationdisclaimer
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D.
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408, +91-7709129400.
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jan 11 2013 - 05:30:03 PST
