[gmx-users] grompp does not find atomtype

[Dawid das]

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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