Dear Prof. Simmerling,
Thank you very much for your advice. I agree that
steric interactions is a real problem and only side
chains of similar shape should be in the multiple
copy. I will use the files generated by addles as a
guide and go from there in modifying the current LES
codes.
Best wishes,
Angela
--- Carlos Simmerling
<carlos.simmerling.stonybrook.edu> wrote:
> Angela,
> the current code is not set up to do that. Older
> versions
> of Amber had something called "chemical monte carlo"
> that
> may do what you want. I think that what you want
> could
> be done if you're willing to change the code, but
> there are
> a few things to consider. For one, since the non-LES
> atoms
> interact with the average energy/force felt between
> them
> and each of the LES copies, you might have steric
> problems.
> For example, if you did Phe and Ser, the other
> groups would bump
> into the Phe ring before they could get close enough
> to
> H-bond to the Ser hydroxyl. Same for Phe and Trp,
> the Phe
> will be in space big enough to hold Trp and the
> other atoms
> could not pack with it.There could be ways to get
> around that,
> but it's a challenge. As far as code changes go I
> think all that
> you need is a program that could make prmtops, the
> actual
> MD code should be fine as it stands if your prmtop
> is
> in standard LES style. Check the Amber web page for
> details on the format, you could use the addles
> program
> as a guide. I think that part is easier than the
> steric problem.
> Carlos
>
> Angela Liu wrote:
>
> >Dear Amber users,
> >
> >The LES program in Amber 8 can do homogeneous
> multiple
> >copy (i.e. same chemical fomula but with different
> >conformation). Let's say I want to create a
> peptide
> >chain in which one residue is a heterogeneous
> multiple
> >copy of several different amino acids. For
> example,
> >one residue can be 50% phenylalanine and 50%
> >tryptophan (both are aromatic). Similar or
> different
> >multiple copies can exist for different residues.
> >What do I need to change to create a proper
> topology
> >file for such multiple copies?
> >
> >Thank you very much for your insight and help!
> >
> >Angela
> >
> >__________________________________________________
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>
> --
>
===================================================================
> 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
>
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>
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Received on Fri Jul 15 2005 - 15:53:00 PDT
