[gmx-users] Error - please help

[Justin A. Lemkul]

Sarina wrote:
> Hello,
> I made a coordinate file of an iron complex and I tried to make the .top file by
> entering:
> g_x2top -f LFe.xyz -o LFE.top 
> and the error I got out was:
> "Could only find a forcefield type for 66 out of 74 atoms"
> where 4 out of those 8 are atoms attached to the metal and the metal itself.  
> I found a couple other people posted similar problems and it was suggested to
> take a look at the .n2t file but I can't find it and if I were to find it I
> wouldn't really know what to do.  Does this sound like a case where I need to
> alter that file and, if so, how do I do that?  Or is there a different solution
> to my problem?

The file format is explained here:

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

Not all force fields have one.  You haven't said which force field you're trying 
to use, but if you can't find one, that's likely the reason.

Deriving parameters for any iron-containing complex may be a futile effort for 
standard MD force fields, for reasons described here:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

-Justin

-- 
========================================

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

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