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

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi,
> 
> first thanks for help. I have two questions.
> 
> 1.) Is this mail going to the mailing list or only to you? If only you 
> get it, how to answer in my thread in the mailig list?
> 

The mail went to the mailing list.  Respond to the post by sending to 
gmx-users at gromacs.org.

> 2.) I add in the beginning of the file ffnonbonded.itp at the beginning 
> in the [ atomtypes ] section following line:
> 
> ;name   at.num  mass    charge  ptype   sigma   epsilon
> CN1B    6       12.01100 0.4925 0.51    A       0.356359487256  0.46024
> 
> If I try to use grompp now, I get the following error. What is wrong?
> 

You have an incorrect number of columns here.  The mass is set to 12.01100, then 
two values are apparently given for charge (0.4925 and 0.51, both of which are 
irrelevant anyway) before the particle type (A) is defined.

With excess parameters, grompp thinks the format is for a different force field, 
so you get this warning:

> WARNING 1 [file ffnonbonded.itp, line 3]:
>   Too few parameters on line (source file
>   /home/me/src/gromacs-4.5.5/src/kernel/toppush.c, line 288)
>
> Generated 20910 of the 20910 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17803 of the 20910 1-4 parameter combinations
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /home/adrian/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
> 

This fatal error arises because the line containing your parameters was not 
properly parsed.  See the existing lines in ffnonbonded.itp and the manual 
(Chapter 5) for proper format.

-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

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