Re: [AMBER] Explicit Solvent Constant pH MD

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 11 Jul 2015 08:50:55 -0400

On Fri, Jul 10, 2015 at 5:52 PM, Rahul Ramesh <raramesh.umich.edu> wrote:

> Thank You, I realized that for the Aspartate residue in residues.py , the
> COOH group is quite different because the two oxygens are connected to two
> hydrogens each. How do I go about generating the prmtop and inpcrd file as
> xleap wouldn't recognize the case where oxygen is connected to two
> hydrogens and a carbon atom.
> I tried an alternate method of generating the partial charges for the
> backbone and CH3COOH group separately and manually entered the partial
> charges in a mol2 file and then used acpype to generate the prmtop and
> inpcrd file. There were lot of zeroes in the prmtop file as some of these
> atom types weren't recognized. I tried generating a cpin file (just to
> try), cpinutils.py did not throw any error but the cpin file was blank.
>

‚ÄčI'm not sure what it is you are trying to do. I would suggest working
through the constant pH tutorials in implicit (
http://ambermd.org/tutorials/advanced/tutorial18/) and explicit (
http://jswails.wikidot.com/explicit-solvent-constant-ph-md) solvent to get
an idea of what to do.

In particular, you need to source the leaprc.constph force field and change
the aspartate residue names to AS4 in the PDB file.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jul 11 2015 - 06:00:03 PDT
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