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
[email protected].
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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