AMBER Archive (2009)

Subject: Re: [AMBER] large resp charges for non-natural amino acid

From: FyD (
Date: Thu Jan 29 2009 - 15:58:34 CST


> I see. I would appreciate lot if you could run RED on the server as we
> still have no access it (my PI asked out legal office to approve the
> usage of RED ... - it takes time). I have two amino acids actually. I
> will attach two tar.gz files. If you could run both or one - great!

ok. We can run both amino acids (AA) in the same R.E.D. Server job. Do
you want also the N-terminal & C-terminal fragments, besides the
central one ? (This is the same amount of work: This will take just
ten minutes on R.E.D. Server). Do you want the version for the Duan et
al FF as well ?

May I ask you to ?
- change the atom order so that you have the following atom order in
your molecules: ACE-AA-NME
  (to not have the NME residue in the middle of the AA residue)
- provide the QM geometry optimization output using
   HF/6-31G* Opt=Tight SCF(Conver=8) or HF/6-31G** Opt=Tight SCF(Conver=8)
  (and not that single point job)
- finally think to the conformation(s) you want to use in the charge
derivation. As you saw the charge value of CA atom oscillate between
0.1 - 0.3 in your case. Usually, one avoids H-bond when selecting a
conformation. You might consider using the ModRedundant mode in
Gaussian to block dihedrals/to remove those H-bonds...

regards, Francois

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