On Fri, Jan 11, 2013 at 2:36 AM, 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?)
>
I think it will cause problems.
Stick to the following command while configuring and then try again
./configure --no-updates gnu
> 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
>
> _______________________________________________
> 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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Received on Thu Jan 10 2013 - 21:30:03 PST
