[gmx-users] grompp does not find atomtype

[Dawid das]

I have just checked with original ffbonded.itp and the onyl difference is
that I added new atomtypes.


2014-06-26 20:58 GMT+02:00 Dawid das <addiw7 at googlemail.com>:

> Thank you so much, but I run into another trouble:
>
> Generated 29890 of the 29890 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 26783 of the 29890 1-4 parameter combinations
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: toppush.c, line: 1631
>
> Fatal error:
> Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
>
>
> So I checked ffbonden.itp :
>
> MCA1    MN1     C       5       121.9           139.746 0.0     0.0
> MN1     C       O       5       122.5           334.720 0.0     0.0
> MN1     C       CT1     5       113.6           334.720 0.0     0.0
> MCA3    MC3     N       5       116.5           334.720 0.0     0.0
> MO3     MC3     N       5       122.5           334.720 0.0     0.0
> MC3     N       H       5       123.0           142.256 0.0     0.0
> MC3     N       CT1     5       120.0           209.200 0.0     0.0
>
> This is under [ angletypes ] for my new atomtypes. There are four
> parameters, so?
> Or perhaps by mistake I deleted something in different line while
> formatting this file?
>
> Best wishes,
> Dawid
>
>
> 2014-06-26 19:48 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
>>
>> On 6/26/14, 1:47 PM, Dawid das wrote:
>>
>>> Dear Gromacs experts,
>>>
>>> I have succesfuly put new atom types into force field expression.
>>> I have managed to run pdb2gms, editconf and genbox.
>>> But when I try
>>> grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o
>>> minimize.tpr
>>>
>>> then I get an error saying that one od my newly inctroduced atoms is not
>>> found... :|
>>>
>>> Fatal error:
>>> Atomtype MH41 not found
>>>
>>> I have checked all of the files once again and it is in atomtypes.atp and
>>> aminoacids.rtp. Also all of the defined parameters use names MH41, MH42
>>> and
>>> MH43.
>>> Why do I get this error?
>>>
>>>
>> atomtypes.atp is only read by pdb2gmx.  You need to add parameters for
>> your new atomtypes in ffnonbonded.itp.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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>
>