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 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.
>
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> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>
>
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>
--
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 - 13:30:03 PST
