[gmx-users] grompp does not find atomtype

[Dawid das]

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.
>
> 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
>
>
> 2014-06-30 14:10 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
>>
>> On 6/30/14, 5:12 AM, Dawid das wrote:
>>
>>> O'right, I'ill do that but I have also noticed visually something
>>> strange.
>>> The thing is that for my new residue there is no bond shown between two
>>> atoms although the distance between them is correct and usual for C-S
>>> single bond.
>>> I used vmd and opened *.gro file. May that be a problem?
>>>
>>>
>> No.  VMD's impression of what a bond is is irrelevant.
>>
>> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
>> Topology_bonds_vs_Rendered_bonds
>>
>>
>> -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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>
>