Thank Jason for your reply, my new input file is following:
Initial minimization in vacuum
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 500,
ntb = 0,
igb = 0,
ntpr = 10,
ntr = 1,
cut = 12,
restraintmask
=':71,83,120,117,329,535.C18,C19,C20,C22,C23,C24,C25,C26,C27,C28,C29,C30,N21,CG,CD1,CE1,CD2,CE2,OH,NE1,CB,CE3,CZ2,CZ3,CH2,OD2,OD1,CZ'
restraint_wt = 500.0
/
END
Fortunately, it works properly.
Regards,
Nguyen Thanh Binh
PhD student, BII, Singapore
Quoting Jason Swails <jason.swails.gmail.com>:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Aug 10 2012 - 20:30:03 PDT
