[gmx-users] grompp does not find atomtype

[Justin Lemkul]

On 6/30/14, 2:23 PM, Dawid das wrote:
> O'right, I have solved this last problem for a new system.
> Here's a link to all the files:
>
> http://www.speedyshare.com/EEXq4/ff-trouble.tar.gz
>
> Thank you for your help!
>
>
> 2014-06-30 18:13 GMT+02:00 Dawid das <addiw7 at googlemail.com>:
>
>> O'right, firstly I have tried to do all the calculations once again for my
>> complete protein system and I got the same error but also something more:
>>
>> ERROR 1 [file mCherry7.top, line 18152]:
>>    No default U-B types
>> ERROR 2 [file mCherry7.top, line 18153]:
>>    No default U-B types
>> ERROR 3 [file mCherry7.top, line 18155]:
>>    No default U-B types
>> ERROR 4 [file mCherry7.top, line 18157]:
>>    No default U-B types
>> ERROR 5 [file mCherry7.top, line 18158]:
>>    No default U-B types
>> ERROR 6 [file mCherry7.top, line 18162]:
>>    No default U-B types
>> ERROR 7 [file mCherry7.top, line 18172]:
>>    No default U-B types
>> ERROR 8 [file mCherry7.top, line 18173]:
>>    No default U-B types
>> ERROR 9 [file mCherry7.top, line 18174]:
>>    No default U-B types
>> ERROR 10 [file mCherry7.top, line 18175]:
>>    No default U-B types
>> ERROR 11 [file mCherry7.top, line 18176]:
>>    No default U-B types
>> ERROR 12 [file mCherry7.top, line 18180]:
>>    No default U-B types
>>
>>
>> Fatal error:
>> Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
>>

This is the only error I can reproduce with the files you posted.  It comes 
directly from the .top file, where you have parameters manually defined.  They 
are defined incorrectly for U-B type angles.

    25    24    26     5    108.4     148.532
    25    24    27     5    108.4     148.532
    25    24    28     5    111.3     192.882
    26    24    27     5    108.4     148.532
    26    24    28     5    111.3     192.882
...
etc.

>> And for my new system, consisting of my new residue and two others at the
>> N and C end I got following error:
>>
>> Fatal error:
>> Unknown bond_atomtype MH1
>>

I can't reproduce this or the first error.  Please be sure to focus questions 
only on what can be reproduced by the files you are providing.  There's no point 
trying to troubleshoot multiple things based on unknown modifications that 
you've made.

-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

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