[gmx-users] grompp does not find atomtype

[Dawid das]

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
>
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> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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