AMBER Archive (2009)

Subject: Re: [AMBER] problem with parametrization

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Jun 25 2009 - 05:04:27 CDT

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:
>
> BOND
> C -n 490.0 1.335 (same as ff99 C-N)
> c -N 490.0 1.335 (same as ff99 C-N)
>
> ANGLE
> 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 <fyd_at_q4md-forcefieldtools.org>:
>
>> 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.
>> http://q4md-forcefieldtools.org/RED/ where RESP inputs are
>> automatically built following a well established approach. Tutorial
>> are available @ http://q4md-forcefieldtools.org/Tutorial/
>>
>> 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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