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

From: FyD <>
Date: Thu, 17 Jul 2014 18:03:29 +0200

Dear Baptiste,

> It works very fine with the RED server following the procedure below. I
> had some missing force field parameters but I found them in the literature.
> If the missing parameters are not available, which solution is the more
> straighforward to obtain them and fill the user.frcmod?

1) look at parameters available in parm99.dat (can be adapted), and by
analogy determine the missing ones (this is what we started to do in
the PyRED source code : this leads to the frcmod.correspondence file)

2) look at parameters available in gaff.dat and by analogy determine
the missing ones (in general they are slightly adapted)

3) compute your own force field parameters - this is particularly
required for key dihedral parameters.

regards, Francois

> Le 16/07/2014 08:20, FyD a écrit :
>> 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
>> 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:
>> vs
>> vs
>> once the job is done you end up with a leap script:
>> See
>> 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 Thu Jul 17 2014 - 09:30:03 PDT
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