[gmx-users] Atomtype not found - grompp - charmm27 and charmm22

[Justin A. Lemkul]

Lara Bunte wrote:
> Hello
> 
> I took parameters that are calculated for  a charmm22 forcefield and I 
> want to use it with a charmm27 forcefield (I have the same molecule as 
> the people who calculated the charmm22 parameters but they didn't use 
> gromacs).  I made a .rtp,  .hdb and residuetypes.dat file and edit the 
> atomtypes.atp file. pdb2gmx works well, also generating a box and use of 
> SPC Water system.  :-)
> 
> The problem starts with grompp. My command was: grompp -f em.mdp -p 
> topol.top -c solvated.gro -o em.tpr
> 
> The Error is:
> 
> Program grompp, VERSION 4.5.5
> Source code file: /home/me/src/gromacs-4.5.5/src/kernel/toppush.c, line: 
> 1166
> 
> Fatal error:
> Atomtype CN1B not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> 
> I read in old mails here in the mailing list and found some similar 
> problems but I don't understood it. Here is my question:
> 
> I know that grompp doesn't use the atomtypes.dat file in which I defined 
> what CN1B is (only pdb2gmx needs it). Where exactly do I have to define 
> my atomtypes for grommp? In a new .itp file, or in my .top file wich 
> pdb2gmx created or in the forcefield files in charmm27 like ffbonded.itp 
> and so on.
> 

The relevant parameters need to be defined in ffnonbonded.itp.

-Justin

-- 
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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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