Try restraintmask and restraint_wt instead of the group input.
HTH,
Jason
On Fri, Aug 10, 2012 at 12:09 PM, Thanh Binh NGUYEN <
nguyentb.bii.a-star.edu.sg> wrote:
>
>
>
> ---------- Forwarded message ----------
> From: Thanh Binh NGUYEN <nguyentb.bii.a-star.edu.sg>
> To: amber.ambermd.org
> Cc:
> Date: Fri, 10 Aug 2012 21:11:42 +0800
> Subject: specific atom restraint
> Dear Amber expert,
> I try to run minimization with some restraint ligand atoms and some
> residues.
> The input file is below.
> Initial minimization in solvent (water)
> &cntrl
> imin = 1,
> maxcyc = 300,
> ncyc = 300,
> ntb = 1,
> ntpr = 10,
> cut = 12,
> ntr = 1
> /
> Keep residue 71 fixed with restraints
> 5000.0
> RES 71
> END
> Keep residue 83 fixed with restraints
> 5000.0
> RES 83
> END
> Keep residue 120 fixed with restraints
> 5000.0
> RES 120
> END
> Keep residue 117 fixed with restraints
> 5000.0
> RES 117
> END
> Keep residue 329 fixed with restraints
> 5000.0
> RES 329
> END
> Restraint atom specification in ligand 535
> 5000.0
> FIND
> * C2 * *
> * N21 * *
> * C3 * *
> SEARCH
> RES 535
> END
> END
>
> For residue restraint, there are no problem, but for ligand atom
> restraint, in the output file it appears like that:
> ----- READING GROUP 6; TITLE:
> Restraint atom specification in ligand 535
>
> GROUP 6 HAS HARMONIC CONSTRAINTS 5000.00000
> ALL ATOMS THAT MEET 1 OF THE FOLLOWING SPECIFICATIONS WILL BE
> INCLUDED IN GROUP BELOW
>
> GRAPH NAME = * SYMBOL = C2 TREE SYMBOL = * RESIDUE
> TYPE = C51
>
> GRP 6 RES 535
> Number of atoms in this group = 0
> ----- END OF GROUP READ -----
> It means that, ligand atoms are not recognized. What should I do to make
> the restraint in some atoms of the ligand?
> Thanks in advance.
> Regards,
> Nguyen Thanh Binh
> PhD student, BII, Singapore.
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 10 2012 - 10:30:04 PDT
