AMBER Archive (2009)

Subject: Re: [AMBER] problem with parametrization

From: janzso_at_brc.hu
Date: Thu Jun 25 2009 - 07:04:27 CDT

Dear Francois,

 From the Gaussian output file I created a prepi file for leap, should
I edit that file, or create a mol2 instead from the Gaussian, and edit
that one?

Thanks,
Gabor

Quoting FyD <fyd_at_q4md-forcefieldtools.org>:

> Gabor,
>
> and what if adding manually FF atom types for your AA* in the Tripos
> mol2 file using Amber99SB ones (i.e. capital letters), load no
> FRCMOD file in a first trial in LEaP, save the prmtop/prmcrd file.
> LEaP is going to tell you which FF parameters are missing. Then, you
> build your frcmod file accordingly to the convention of Amber99SB
> and load it in LEaP.
>
> regards, 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
>>
>> and
>> "CT-C-n-c3"
>> "o-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:
>>
>> DIHE
>> 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,
>> Gabor
>>
>>
>>
>>
>> Quoting FyD <fyd_at_q4md-forcefieldtools.org>:
>>
>>> 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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>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
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>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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