You can use ptraj to truncate your system, but then you'll have to create a
matching topology file. I'll bet VMD can also output a partial PDB of a
subset of your system based on some distance criteria.
My advice is to use nab's nmode functionality rather than nmode itself. It
is described in the AmberTools manual.
Good luck!
Jason
2010/11/18 xuemeiwang1103 <xuemeiwang1103.163.com>
> I have got the answer ,we can do this by using Pymol : )
> At 2010-11-17 20:37:20，xuemeiwang1103 <xuemeiwang1103.163.com> wrote:
> >Dear All :
> > I try to use nmode to calculate entropy.But I got the following
> error message:
> > PARM file has the title
> >Total memory required : 1163578999 real words
> >Total memory required : 43660952 integer words
> >Total memory required : 28430 4-character words
> >Maximum nonbond pairs 43073120
> >ASSERTion ' ier == 0 ' failed in nmode.f at line 106.
> > I checked the maling list and got the ideal that the memory is not
> enough for my system (about 8000 atoms). In order to solve this ,I want to
> truncate the protein to contain only residues within 8A of the ligand.There
> is a paper which sugest me to use the changepdb command ,but I didn't find
> the comand in the Amber procedure.Could someone give me some ideals about
> this ? Thanks !
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Nov 18 2010 - 07:30:26 PST
