[gmx-users] Urea topology problem

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

<snip>

> 
> ERROR 1 [file solvated.top, line 39]:
> 
>   atom C1 (Res UREA-1) has mass 0
> 
>  

In urea.itp, no masses are defined.  If you correct the format of this file (see 
Chapter 5 of the manual), then this issue should be resolved.


> 
> Which force field does this urea.itp correspond to? Where should it look 
> for the atomtypes of urea?
> 
>

The .atp file corresponding to the force field you are using (ffG43a2).  The 
atomtypes for urea appear to be generic for use with the Gromos96 force fields. 
  There are specific atomtypes within ffG53a6 for urea, if you want to use the 
newer force field (check the ffG53a6.rtp file for the urea parameters).

-Justin


> 
> Thank you very much for your help,
> 
>  
> 
> Rebeca Garcia
> 
> Parc Cientific de Barcelona
> 
> regafan at hotmail.com
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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