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