[gmx-users] grompp does not find atomtype

[Justin Lemkul]

On 6/26/14, 3:15 PM, Dawid das wrote:
> 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.
>

If the force field you're using uses U-B angles, you should stick to that.  If 
you don't need the cross-term, just specify ub0 and kub as zero, while leaving 
sensible values for theta0 and ktheta.

-Justin

>
> 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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>>>
>>>
>>

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

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

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