[gmx-users] Atomtype HW not found when using grompp for energy minimization

[Justin A. Lemkul]

Parul tew wrote:
> Hello,
> I get the following error when I try to run grompp cpmmand for energy
> minimization in GROMACS of DPPC membrane
> ...............................................................................
> checking input for internal consistency...
> processing topology...
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 843
> 
> Fatal error:
> Atomtype HW not found
> 
> 

Per the tutorial, step 2: "Non-bonded interactions involving atom type HW are 
also present; since these are all zero you can delete these lines as well, or 
otherwise rename HW as H to be consistent with the GROMOS96 53a6 naming convention."

> the topology file of the DPPC contains:
> ------------------------------------------------------------------------------------------
> ;       This is your topology file
> ;       1SOL     OW    1  -2.449  -4.190  -1.80
> ;
> ; Include chain topologies
> #include "ffG53a6_lipid.itp"
> #include "dppc.itp"
> 
> ; Include water topology
> ;include "spc.itp"
> 
> ; Include ion topologies
> ;include "ions.itp"
> 

You're going to have problems here, as well.  You've commented out the water and 
ion topologies.  The next fatal error is surely going to be "Moleculetype SOL 
not defined" or the like.

-Justin

> ; System specifications
> [ system ]
> 128-Lipid DPPC Bilayer
> 
> [ molecules ]
> ; molecule name nr.
> DPPC 128
> SOL 3655
> ------------------------------------------------------------
> I am using ffG53a6
> thanks
> 
> 

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

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

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