[gmx-users] error with x2top.

[Justin Lemkul]

On 9/25/12 4:28 PM, Elie M wrote:
>
> Dear all,
> i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error:
> Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 with................Fatal error:Could only find a forcefield type for 73 out of 94 atoms
> I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol?  Is there any clear examples of how to do this? Any help would be appreciated. Thanks
>

The format is explained in full here:

http://www.gromacs.org/Documentation/File_Formats/.n2t_File

The charges and atom types are determined by parameterizing the molecule of 
interest, but if you're going to do that much work, it's probably simpler to 
create an .rtp entry and have pdb2gmx do the work.  g_x2top is usually intended 
to create simple topologies for simple molecules.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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