Re: [AMBER] To get resp charges of a modified central residue (not an integer).

From: FyD <>
Date: Wed, 16 Jul 2014 08:20:58 +0200

Dear Baptiste,

The total charge of a molecular fragment originating from a molecule
has to be an integer, and this can be only achieved by applying
specific charge constraint(s) during the charge fitting step.

You could use R.E.D. Server Dev./PyRED at

See the corresponding tutorial:

PyRED generates an empirical force field (force field libraries +
force field parameters) and a LEaP script for input molecules and
molecular fragments.

In your case read:

once the job is done you end up with a leap script:

    tar -jxvf P$x.tar.bz2
    cd P$x/Data-R.E.D.Server/Data-Default-Proj
    xleap -f leaprc.q4mdfft

That means no need to load gaff + amber99 + whatever additional force
field_s_ and no need to load tons of useless atom types ;-)
A single force field is generated based on parm99, and a user can even
provide missing and/or mandatory force field parameters as input via
the frcmod.user file (see
Thus only required force field atom types/parameters are generated
(generic dihedral force field parameters are also converted into
specific ones to prepare MM vs QM dihedral fit etc...).

I hope this helps...

regards, Francois

> I tried diverses strategies to get resp charges of an exotic amino acid
> (a dipeptide actually) and to incorporate it in a peptide sequence but
> without success (not an integer) . Can you give me your opinion, please?
> For example:
> First, I built a pdb of my modified residue (NH2-MOD-COOH) then I
> launched antechamber:
> antechamber -i MOD.pdb -fi pdb -o ./MOD.prepin -fo prepi -c bcc -s 2 >
> antechamber.out
> parmchk -i MOD.prepin -f prepi -o MOD.frcmod (and I completed the frcmod
> file manually to fit parm99.dat)
> In parallel, I built the ACE-MOD-NME fragment (MOD-cap.pdb) to derive
> the charge using the RED server and to modify the charges directly in
> the prepin.
> Then, I used leap:
> source leaprc.gaff
> source leaprc.ff99SB
> loadamberprep MOD.prepin
> loadamberparams MOD.frcmod
> remove MOD MOD.1.H29 (remove a H from the NH2)
> remove MOD MOD.1.H30 (remove the H from the COOH)
> set MOD head MOD.1.N1
> set MOD tail MOD.1.C5
> tri = sequence { NALA MOD CALA}
> saveamberparm tri tri.prmtop tri.inpcrd
> Finally, except the charges, the generated files seems to be correct. I
> also tried to calculate the charges only using antechamber and/or via a
> mol2 file generating a new library.

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Received on Tue Jul 15 2014 - 23:30:03 PDT
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