page 119 in the manual (under "distance, angle and dihedral restraints")
L Jin wrote:
>Thank you very much for reply.
>
>It seems to me that the makeCHIR_RST command is used to generate dihedral
>restraint for amino acids only. But my molecule is a disaccharide. And I want
>to fix the two dihedral angles across the glycosidic linkages.
>
>When I used the makeCHIR_RST and a pdb input file, it returned nothing in the
>output file. So I turned to use the Cartesian coordinate restraints. I tried 50
>just now but still not restrain the atoms moving.
>
>Is there any other method to do this kind of minimization with restraint of
>dihedral angles for saccharide within AMBER? By the way, is it reasonable to
>use
>Cartesian coordinate restraints to restrain a dihedral angle?
>
>Many thanks.
>
>
>Quoting Carlos Simmerling <carlos.ilion.bio.sunysb.edu>:
>
>
>
>>1) you're using Cartesian coordinate restraints to restrain a dihedral
>>angle-
>>why not just use dihedral angle restraints? check the sander manual for
>>details
>>
>>2) if you want to keep using the Cartesian restraints,
>>you might need a strong force constant than 1.0 to keep the atoms from
>>moving, try using 10 or 50 and see if that helps.
>>
>>===================================================================
>>Carlos L. Simmerling, Ph.D.
>>Associate Professor Phone: (631) 632-1336
>>Center for Structural Biology Fax: (631) 632-1555
>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
>>===================================================================
>>
>>
>>
>>
>>L Jin wrote:
>>
>>
>>
>>>Dear AMBER users,
>>>
>>>I am using AMBER7 and trying to run restraint minimization with the
>>>
>>>
>>following
>>
>>
>>>input file so that I can fix the five atoms which defined two dihedral
>>>
>>>
>>angles.
>>
>>
>>>I used the initial structure coordinate file as the reference for the
>>>restraint. But when I checked the ouput structure, the dihedral angles,
>>>
>>>
>>which
>>
>>
>>>are supposed to be fixed, actually changed. Did I do something wrong or not
>>>successfully define the restraint? Could anybody give me some suggestions?
>>>
>>>
>>Many
>>
>>
>>>thanks in advance.
>>>
>>>Minimization with sander (Amber7)
>>>&cntrl
>>> imin = 1, maxcyc = 50000, drms = 0.0005, ntb = 0,
>>> ntpr = 100, cut = 999., ncyc = 1000, ntr=1,
>>>&end
>>>Group input for restrained atoms of dihedral angles
>>>1.0
>>>ATOM 28 32
>>>END
>>>END
>>>
>>>
>>>Lan
>>>
>>>
>>>
>>>
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>>
>>
>
>
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Received on Tue Feb 22 2005 - 17:53:00 PST
