Hi,
For idecomp=1 I think you define ligand and receptor residues with
LRES and RRES respectively; RES determines which residues have
information printed. So I think you may want something like:
Receptor residues
RRES 1 123
END
Ligand residue
LRES 124
END
Print All Residues
RES 1 124
END
END
-Dan
On Sat, Feb 9, 2013 at 9:55 PM, Adam Mepham <amepham.sympatico.ca> wrote:
> Hello,
>
> I am attempting to run a sander simulation with idecomp. My input file
> is as follows:
>
> title
> &cntrl
> nstlim =1, nscm=2000,
> ntx=1, irest=0, ntpr=1000,
> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
> ntb=0, igb=5, cut=999.0,
> dt=0.001,
> idecomp=1,
> ntc=2, ntf=2,
> ntwr = 10000, ntwx=1000, ntave=1000
> /
> Some residues
> RES 1 123
> END
> Some other residues
> RES 124
> END
> END
>
>
>
>
>
> However, it appears that the final END card is being seen as a third
> group title, because my output is as follows:
>
> LOADING THE DECOMP ATOMS AS GROUPS
>
> ----- READING GROUP 1; TITLE:
> Some residues
> GRP 1 RES 1 TO 123
> Number of atoms in this group = 1840
> ----- READING GROUP 2; TITLE:
> Some other residues
> GRP 2 RES 124 TO 124
> Number of atoms in this group = 17
> ----- READING GROUP 3; TITLE:
> END
>
> rfree: End of file on unit 5
>
>
>
>
> Any suggestions?
>
>
> --
> Sincerely,
> Adam
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Sun Feb 10 2013 - 10:30:03 PST
