On Wed, Nov 7, 2012 at 4:12 AM, baogen duan <dbaogen.gmail.com> wrote:
> Dear Bill,
>
> Thank you for your reply. But I still have some puzzle about
> this. If I upgrade to AmberTools 12, whether should I correspondingly
> upgrade Amber 11 to Amber 12?
>
> I also have try some tests using sander program in Amber 11 to
> carry out minimization or MD simulation, and the input prmtop and
> inpcrd are generated by Chamber program. For the small ligand molecules,
> minimization and MD is Ok. But for receptor and complex, the output file of
> minimizaiton and MD shows the same error as MMPBSA calculation. the error
> is also:
>
> rdparm: a parameter array overflowed
> (e.g. the table of dihedral params)
> NUMBND = 133 max is 5000
> NUMANG = 297 max is 900
> NPTRA = 612 max is 1200
> NATYP = 72 max is 100
> NPHB = 0 max is 200
> NTTYP = 2628 max is 1830
>
This is your problem. The maximum nttyp parameter is 1830. Note this is a
very large number of atom types, so something here seems strange (this
represents the VDW parameter types). A typical number of types in this
case is ~20-30 in typical Amber topologies.
You can change "1830" in parms.F90 and rdparm.F90 ($AMBERHOME/src/sander)
and see if that helps, but you should check the results from your topology
file carefully.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 07 2012 - 11:30:04 PST
