Hi,
What version of Amber are you using and what bugfixes have been
applied? Also, do all of your test cases pass (particularly the MMPBSA
tests)? Have you tried running serial MMPBSA as well?
-Dan
On Sun, Feb 3, 2013 at 2:55 PM, <psu4.uic.edu> wrote:
> Dear Amber,
>
> Here is the more detailed input:
>
> ibrun MMPBSA.py.MPI -O -i mmgbsa.in -o result.dat -sp
> protein_ligand_12A.prmtop -cp protein_ligand.prmtop -rp protein.prmtop -lp
> ligand.prmtop -y protein_ligand_12A.mdcrd
>
> For mmgbsa.in
>
> Input file for running mmPBSA
> &general
> keep_files=2,use_sander=1,
> /
> &gb
> igb=7, saltcon=0.100
> /
>
> The issue only occurs if I use igb=7 or 8. igb=1,2,5 are fine.
>
> Thanks.
>
> Cheers,
> Henry
>
> On Sat, Feb 2, 2013 at 9:08 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> That's your entire input?
>> On Feb 2, 2013 6:50 PM, <psu4.uic.edu> wrote:
>>
>> > Dear Amber,
>> >
>> > When we use igb=7 or 8, there is an error message:
>> > CalcError: "pathway" failed with prmtop "protein".prmtop.
>> > error occured on rank "number".
>> >
>> > However, we don't encounter the same issue in igb=1 or 2 or 5.
>> >
>> > Here is the input file for igb=7 & 8
>> >
>> >
>> >
>> > &general
>> > keep_files=2, use_sander=1,
>> > /
>> > &gb
>> > igb=7, saltcon=0.100,
>> > /
>> >
>> >
>> >
>> > Could someone help out? Thanks.
>> >
>> > Cheers,
>> > Henry
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Feb 04 2013 - 08:00:05 PST
