On Jan 11, 2013, at 12:53 AM, JD John wrote:
> Dear all,
>
> I want to get the coordinate and parm file for
> a new system with Folic Acid. I have a pdb file (attached)
> of folic acid but it is not not recognized by xleap.
>
> If some one has simulated it before or have any idea
> to get these files, kindly help me.
>
The first problem I see is that the molecule in the PDB file
has no hydrogens. AMBER assumes the molecules to be properly
represented. Look on the AMBER web site for tutorials about
creating all the force field files for new residues and
molecules. The web site of the q4md project,
http://q4md-forcefieldtools.org/ can be enormously helpful.
To find groups that might have done MD on FA before, google
is your friend. Search terms probably should contain:
"folic acid" amber
HTH
Bud Dodson
> Thanks
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
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Received on Fri Jan 11 2013 - 06:00:06 PST
