Re: [AMBER] Non-Standard Residues Problems

From: FyD <>
Date: Thu, 30 Jun 2011 21:38:21 +0200


> Another thing we've done is optimized and calculated the energy and charges
> of the Ser-PPP resiude in Gamess.

With R.E.D. Server, you can use Gaussian 2003, Gaussian 2009,
Gamess-US or Firefly.

> But then how do I make the mol2 file and frcmod files?

     R.E.D. Server allows:
      (A) Ante_R.E.D. 2.0
PDB files(s) ---> P2N file(s)
                                  (i) geometry optimization
                                 (ii) MEP computation
      (B) R.E.D. IV: four steps (iii) charge fitting
                                 (iv) ff lib. building
P2N files(s) ---> mol2 file(s)


A frcmod file contains missing force field parameters. If needed, it
can be generated independently of the FF libraries by hand by looking
at errors generated by LEaP or by using Antechamber.

> To have closed shells I added extra hydrogens to the Ser where it would be
> joined with the other amino acids.

You can add hydrogen in your PDB file by using R.E.D. Server as well.

regards, Francois

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Received on Thu Jun 30 2011 - 13:00:04 PDT
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