Yes, you can use the -cp flag to specify the prmtop file for stability calculations (calculations without a receptor or ligand).
-Bill
On Sep 6, 2012, at 6:59 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Hello Mr. Jason,
> In MMPBSA.py command line there is no -p flag
> to specify prmtop file. The system I am using is a protein only, not a
> complex. It is a metalloprotein. Here I have used -cp flag to
> introduce prmtop file. Can I use it safely?
>
> Sanjib
>
> On 9/5/12, Jason Swails <jason.swails.gmail.com> wrote:
>> On Wed, Sep 5, 2012 at 8:59 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
>>
>>> Dear Amber Users,
>>> I want to calculate normal modes of my
>>> system by NAB using AmberTools12. My input file is like following.
>>>
>>> molecule m;
>>> float x[4103], fret;
>>>
>>
>> Your coordinate array must be set to hold 3*natom coordinates. If you have
>> 4103 atoms, you will need an array with 12309 floating point values.
>> Otherwise you will get a segfault.
>>
>> readparm(m,"protein.prmtop");
>>>
>>
>> The molecule "m" needs to be initialized with a PDB file first, I believe.
>>
>>
>>> mm_options("cut=99., ntpr=50");
>>> mme_init(m, NULL, "::z", x, NULL);
>>> setxyz_from_mol(m, NULL, x );
>>>
>>> // conjugate gradient minimization
>>> conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000);
>>>
>>
>> You should probably use the xmin minimizer to prepare for normal mode
>> analysis -- it does a much better job of getting close to a minimum.
>>
>> My suggestion is to either use MMPBSA.py to do your nmode calculations for
>> you, or look at mmpbsa_entropy.nab in $AMBERHOME/AmberTools/src/mmpbsa_py
>> and either use that program directly or adapt it for your needs.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
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>>
>
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Received on Thu Sep 06 2012 - 05:30:02 PDT
