[gmx-users] atomtype c3 not found

[Justin Lemkul]

On 4/7/14, 8:55 AM, chetan kumar meena wrote:
> can't you go with other force field. you can use gromos force field and for
> that PRODrug tool is there which generates parameter for small molecular
> for gromos force field.
>

PRODRG generates flawed parameters.  Combining GAFF ligand topologies with a 
parent AMBER force field is easy to do; it's just a matter of getting the 
topology format correct.

-Justin

>
> On Mon, Apr 7, 2014 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/7/14, 7:48 AM, Monoj Mon Kalita wrote:
>>
>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Mon, 7 Apr 2014 12:50:21 +0200
>>>> From: Mark Abraham <mark.j.abraham at gmail.com>
>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> Cc: Discussion list for GROMACS users
>>>>           <gromacs.org_gmx-users at maillist.sys.kth.se>
>>>> Subject: Re: [gmx-users] atomtype c3 not found
>>>> Message-ID:
>>>>           <
>>>> CAMNuMAR+26NRUYM85KvoUKrgKFn4nr6BHfvwFBujtxhTNuCJ6A at mail.gmail.com>
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>>
>>>> On Mon, Apr 7, 2014 at 11:22 AM, Monoj Mon Kalita <mon.123chem at gmail.com
>>>>
>>>>> wrote:
>>>>>
>>>>
>>>>   Dear users
>>>>>
>>>>> I am trying to simulate a ligand and protein in POPC. I have calculated
>>>>>
>>>> the
>>>>
>>>>> ligand paramteres using the generalized amber force field (GAFF)  and
>>>>>
>>>> now I
>>>>
>>>>> am trying to simulate the ligand-protein system with amber99sb-ildn ff.
>>>>>
>>>>    I
>>>>
>>>>> have added the lines in the topology file like this
>>>>>
>>>>>
>>>>> ; Include forcefield parameters and compound atomtypes
>>>>> #include "amber99sb-ildn.ff/forcefield.itp"
>>>>> #include "ligand-non-bonded.itp"
>>>>>
>>>>> ; Include chain topologies
>>>>> #include "topol_Protein.itp"
>>>>>
>>>>> ; Include water topology
>>>>> #include "amber99sb-ildn.ff/spc.itp"
>>>>> ;Include ion parameters
>>>>> #include "amber99sb-ildn.ff/ions.itp"
>>>>>
>>>>> ;Include compoud
>>>>> #include "ligand.itp"
>>>>>
>>>>> [ system ]
>>>>> ; Name
>>>>> protein
>>>>>
>>>>> [ molecules ]
>>>>> Protein
>>>>> SOL
>>>>> MOL
>>>>>
>>>>> But the grompp is not reading the ligand parameters. It is showing the
>>>>> error 'atomtype c3 not found'.
>>>>>
>>>>>
>>>> That kinda means what it says. ligand-non-bonded.itp is supposed to be
>>>> doing that definition, so have a look inside it and decide who is not
>>>> matching who, and why.
>>>>
>>>> Mark
>>>>
>>>>
>>>> Yes, I know that. But, my question was is there any other method to
>>>> define
>>>>
>>> these new atom types as they are not implemented in amber99sb-ild.ff of
>>> gromacs. I tried to define them in ffnonbonded.itp file. Then that error
>>> doesn't appear, but after performing genion step I get a broken molecule,
>>> means gromacs ignores the connections of my ligand.
>>>
>>>
>> There are two options:
>>
>> 1. Add the new atomtypes to ffnonbonded.itp
>> 2. #include a file with an [atomtypes] directive
>>
>> Both approaches are equivalent, and neither will lead to a "broken"
>> molecule at any point, because neither relates to periodicity or bonded
>> geometry.
>>
>> -Justin
>>
>>
>>
>>>
>>>>> These are the atomtypes in my ligand file from GAFF
>>>>>
>>>>>    c3       c3          0.00000  0.00000   A     3.39967e-01
>>>>> 4.57730e-01
>>>>>
>>>> ;
>>>>
>>>>> 1.91  0.1094
>>>>>    n3       n3          0.00000  0.00000   A     3.25000e-01
>>>>> 7.11280e-01
>>>>>
>>>> ;
>>>>
>>>>> 1.82  0.1700
>>>>>    hc       hc          0.00000  0.00000   A     2.64953e-01
>>>>> 6.56888e-02
>>>>>
>>>> ;
>>>>
>>>>> 1.49  0.0157
>>>>>    hn       hn          0.00000  0.00000   A     1.06908e-01
>>>>> 6.56888e-02
>>>>>
>>>> ;
>>>>
>>>>> 0.60  0.0157
>>>>>
>>>>> which are already in the ligand-non-bonded.itp file.
>>>>>
>>>>> Can anybody suggest me, how to solve this issue. I have seen this issue
>>>>>
>>>> in
>>>>
>>>>> the archive, but didn't find much information in it.
>>>>>
>>>>> http://comments.gmane.org/gmane.science.biology.gromacs.user/41031
>>>>>
>>>>>
>>>>> with regards
>>>>>
>>>>> Mon
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>>
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================