Quoting janzso.brc.hu:
> 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?
I guess you should be able to generate a Tripos mol2 file from Antechamber.
Or you could use LEaP.
See
http://q4md-forcefieldtools.org/Tutorial/leap.php
regards, Francois
> Quoting FyD <fyd.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.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.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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Received on Mon Jul 06 2009 - 11:14:58 PDT
