AMBER Archive (2009)

Subject: Re: [AMBER] problem with parametrization

Date: Thu Jun 25 2009 - 06:40:35 CDT

Dear Francois,

So if my modifications might work, I have only one more question left:
I searched thoroughly the parm99.dat file, but I cannot find these
dihedral parameters (or maybe I don't know which ones are used by leap
for these dihedrals):
   O-C-n-c3 o-c-N-CT
   CT-C-n-hn c3-c-N-H


I paired the first four, because they seem to refer the same dihedral.
For these I could not find the adequate parameters in parm99.dat
(neither in gaff.dat for that matter). Maybe you can tell me which
ones are used in the amber99SB force field? It should be there,
because they are part of a simple peptide bond.

The peculiar thing is with the two dihedrals I put in quotation marks,
that they are defined in my frcmod file like this:

O -C -n -hn 1 2.50 180.0 -2 same as ff99 H -N -C -O
o -c -N -H 1 2.50 180.0 -2 same as ff99 H -N -C -O
CT-C -n -c3 4 10.00 180.0 2. same as ff99 X -C -N -X
c3-c -N -CT 4 10.00 180.0 2. same as ff99 X -C -N -X

I copied these parameters from the parm99.dat file just like the
others, but it seems that only one of each pair is accepted/recognized
by leap, could you tell me what did I do wrong? I am not even sure why
dihedrals have four parameters, not just two as the bonds and angles do.

Best regards,

Quoting FyD <>:

> Dear Gabor,
>> Thanks for the heads-up, I actually already spotted that charge problem
>> as well, but I think I know what have I done wrong, so hopefully I can
>> fix it.
>> On the other hand, you say it won't work what I intended to do? My plan
>> was that in the frcmod file, I define parameters for the missing bonds
>> and angles like this:
>> C -n 490.0 1.335 (same as ff99 C-N)
>> c -N 490.0 1.335 (same as ff99 C-N)
>> O -C -n 80.0 122.90 (same as ff99 N -C -O)
>> o -c -N 80.0 122.90 (same as ff99 N -C -O)
>> .
>> .
>> .etc
>> So if I copy the parameters from parm99.dat (because these parameters
>> are not modified in the ff99SB force field) and define the missing
>> parameters, as I showed above, the calculation wouldn't work? If I
>> understand you correctly, you meant something like this when you
>> suggested that I should use Amber99SB force field parameters.
> I never did that, but your modifications seems perfect.
> These look like "aliases" between GAFF & Amber99SB ;-)
> regards, Francois
>> Quoting FyD <>:
>>> Dear Gabor Janzso,
>>> You want to connect your modified amino-acid* AA* to other amino-acids AAs.
>>> Amber99SB is used for AAs. Consequently, you have to use parm99SB
>>> for AA* as well.
>>> You can indeed mix GAFF and Amber99SB i.e. 2 different force
>>> fields ONLY when you have for instance a ligand and a protein
>>> i.e. NO CONNECTION between the ligand and the protein.
>>> When you have a connection "between two different parts" (in your
>>> case the two different parts are indentical as AA) you have to
>>> use the same FF.
>>> As an example:
>>> - Could not find bond parameter for: C - n
>>> => Not possible: Amber99SB + GAFF impossible because of the connection
>>> - Could not find bond parameter for: C - N
>>> => possible: all Amber99SB => this is what you need
>>> or
>>> Could not find bond parameter for: c - c
>>> => possible: all GAFF => You cannot use that in your case
>>> You have to use Amber99SB for all your peptide/protein.
>>> I think Antechamber has been designed (i) for organic molecules
>>> (ii) to be connected with GAFF. You can use GAFF in some cases;
>>> not in your case.
>>> Then, if I continue, your have this error:
>>>> ERROR: The unperturbed charge of the unit: -0.107460 is not integral.
>>> Here, there is another problem, you should have an integer value.
>>> This likely means your charge fit did not work or some
>>> constraints you used are wrong.
>>> I strongly suggest you to use R.E.D.
>>> where RESP inputs are
>>> automatically built following a well established approach.
>>> Tutorial are available @
>>> regards, Francois
>>>> I am trying to create a non-standard residue with antechamber to use it
>>>> in tleap. This residue is the isopeptide form of the gly-ser dipeptide,
>>>> where the carbonyl group of the glycine is attached to the -OH group of
>>>> the serine sidechain. I have created and parametrized this molecule
>>>> following the antechamber tutorial for creating non-standard residues,
>>>> I also created an frcmod file with parmchk. But when I try to build a
>>>> polipeptide chain using my new residue, leap complains about missing
>>>> parameters. Basically the missed parameters are at the joining points
>>>> of my residue with the rest of the polipeptide.
>>>> The message goes like this (I built a tripeptide in this example after
>>>> loading leaprc.gaff and leaprc.ff99SB):
>>>>> loadamberparams glyser.frcmod
>>>> Loading parameters: ./glyser.frcmod
>>> => the "glyser.frcmod" file generated by Antechamber cannot be
>>> used in your case.
>>>> Reading force field modification type file (frcmod)
>>>> Reading title:
>>>> remark goes here
>>>>> loadamberprep glyser.prepi
>>>> Loading Prep file: ./glyser.prepi
>>>>> aa = sequence { ALA GSD ALA }
>>>>> saveamberparm aa proba.prmtop proba.inpcrd
>>>> Checking Unit.
>>>> ERROR: The unperturbed charge of the unit: -0.107460 is not integral.
>>>> WARNING: The unperturbed charge of the unit: -0.107460 is not zero.
>>> => an error here. The charge fit did not work.
>>>> -- ignoring the error and warning.
>>>> Building topology.
>>>> Building atom parameters.
>>>> Building bond parameters.
>>>> Could not find bond parameter for: C - n
>>> => impossible
>>>> Could not find bond parameter for: c - N
>>> => impossible
>>>> Building angle parameters.
>>>> Could not find angle parameter: O - C - n
>>> => etc
>>>> Could not find angle parameter: C - n - hn
>>>> Could not find angle parameter: C - n - c3
>>>> Could not find angle parameter: CT - C - n
>>>> Could not find angle parameter: o - c - N
>>>> Could not find angle parameter: c - N - H
>>>> Could not find angle parameter: c - N - CT
>>>> Could not find angle parameter: c3 - c - N
>>>> Building proper torsion parameters.
>>>> ** No torsion terms for O-C-n-hn
>>>> ** No torsion terms for O-C-n-c3
>>>> ** No torsion terms for CT-C-n-hn
>>>> ** No torsion terms for CT-C-n-c3
>>>> ** No torsion terms for o-c-N-H
>>>> ** No torsion terms for o-c-N-CT
>>>> ** No torsion terms for c3-c-N-H
>>>> ** No torsion terms for c3-c-N-CT
>>>> Building improper torsion parameters.
>>>> old PREP-specified impropers:
>>>> <GSD 2>: C3 O2 C4 O3
>>>> <GSD 2>: +M C6 C7 O4
>>>> total 5 improper torsions applied
>>>> 2 improper torsions in old prep form
>>>> Building H-Bond parameters.
>>>> Parameter file was not saved."
>>>> Since I want to use the force field ff99SB for my calculations, and the
>>>> isopeptide residue was parametrized using gaff the missing parameters
>>>> are aviable at both force field, but not recognized because of the
>>>> capitalization. I figured I can modify the frcmod file to have leap
>>>> handle these angles and bonds and dihedrals, but I could not find some
>>>> of the dihedral parameters, neither in parm99.dat or gaff.dat:
>>>> O-C-n-c3
>>> => impossible
>>>> CT-C-n-hn
>>> => etc..
>>>> CT-C-n-c3 o-c-N-H o-c-N-CT c3-c-N-H Could you tell me
>>>> where can I find these parameters, or what parameters
>>>> should I use?
>>> You have to use Amber99SB force field parameters. Antechamber
>>> generates GAFF force field parameters.
>>>> Thanks in forward:
>>>> Gabor Janzso
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