Hi Jason,
I updated to AMBER14Tools and I am still getting an error.
This time:
File "/global/software/amber/amber14/bin/MMPBSA.py", line 96, in ?
app.run_mmpbsa()
File "/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/calculation.py",
line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/calculation.py",
line 147, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /global/software/amber/amber14/bin/sander failed with prmtop
./nw.complex.top!
Exiting. All files have been retained.
My system contains MNG and so I tried once stripping MNG and once without
stripping it, and either way I get the same error. Should it be necessary
to strip the Manganese ions?
I appreciate your help.
Regards,
Holly
On Mon, Aug 18, 2014 at 10:58 AM, Hallel Freedman <hfreedma.ualberta.ca>
wrote:
> Thank you Jason, I'll try again with AMBER14.
> Regards,
> Holly
>
>
>
> On Mon, Aug 18, 2014 at 5:14 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Sun, 2014-08-17 at 16:42 -0600, Hallel Freedman wrote:
>> > Dear AMBER,
>> > I am getting an error when trying to run MMGBSA with the idecomp
>> keyword.
>> > The error message says:
>> >
>> > CalcError: /global/software/amber/amber13/bin/sander failed with prmtop
>> > ./nw.complex.top!
>> > Exiting. All files have been retained.
>> >
>> > Looking into _MMPBSA_gb_decomp_com.mdin, I have
>> >
>> > File generated by MMPBSA.py
>> > &cntrl
>> > ncyc=0, cut=999.0, nsnb=99999, gbsa=2,
>> > saltcon=0.15, ntb=0, dec_verbose=0,
>> > imin=5, idecomp=1, extdiel=80.0,
>> > igb=2, surften=0.0072,
>> > /
>> > Residues considered as REC
>> > RRES 1 500
>> > END
>> > Residues considered as LIG
>> > LRES 501 501
>> > END
>> > Residues to print
>> > RES 1 1 499 499
>> > END
>> > END
>> > bad atom type: o
>> >
>> >
>> > I know that similar errors have been reported, but I still can't figure
>> out
>> > what's happening here.
>>
>> This is being hit because the ICOSA surface area parameter for the atom
>> type "o" is not programmed into sander. However, as of AmberTools 14
>> (as well as some earlier versions, I think), these parameters are
>> assigned based on the atomic number rather than the atom type, and I
>> would have assumed that the type "o" would have been assigned the atomic
>> number of 8 for Oxygen. In this case, oxygen parameters are defined and
>> you should not be hitting this error.
>>
>> The fact that you are suggests to me that you are using an older version
>> of AmberTools (i.e., AmberTools 12 or earlier) and that this problem
>> would be solved by upgrading to the latest version of AmberTools and
>> trying again.
>>
>> It's always a good idea to tell us what version of Amber you're using
>> when asking for help, so we don't have to try and guess ;). You should
>> also include all of the bug fixes and updates that have been applied --
>> you can type "$AMBERHOME/update_amber --version" to get this
>> information. This is always good information to include when reporting
>> a problem (even better would be to check the list of updates and see if
>> your problem may have already been addressed).
>>
>> HTH,
>> Jason
>>
>> > I would very much appreciate any suggestions on this.
>> > Thanks,
>> > Holly
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Wed Aug 20 2014 - 10:00:02 PDT
