[gmx-users] grompp does not find atomtype

[Dawid das]

I have figured out that I don't really need those U-B parameters, so I
changed function type to 1, and deleted those two last columns of zeros.
But I still get exactly the same error.


2014-06-26 21:05 GMT+02:00 Dawid das <addiw7 at googlemail.com>:

> 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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>>
>>
>