Mr Bernard Ramos wrote:
Hi everyone!
I added a residue on the gromacs 4.5.3 I have. I followed the
instructions as indicated in the "Adding A Residue to a Force Field"
with this link
_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_.
I added the residue to residuetypes.dat and indicated it as a
carbohydrate. The topology in fact was able to write it down as a
carbohydrate.
Carbohydrates should be grouped into the "other" category; I'm not sure
"Carbohydrate" is a recognized type. What do you mean the topology wrote it as
a carbohydrate? Is that the [moleculetype] name it was given the topology?
__
Generating a topology went well with pdb2gmx, editconf, genbox, energy
minimization. However, I encountered the following error when I was
about to do an NVT equilibration.
----------------------------------------------------------------------------------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: readir.c, line: 1316
Fatal error:
Group protein not found in indexfile.
Maybe you have non-default groups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n'option.
----------------------------------------------------------------------------------------------------------------------------------
In response, I created an index file using make_ndx. The index file was
able to generate correctly the molecule indices and identified it
correctly as indicated in the residuetypes.dat and carbohydrate.rtp
Your error does not appear to be connected to the carbohydrate at all. The
problem appears to be the use of "protein." Capitalization shouldn't matter, so
I'm not sure why grompp is complaining.
And then I tried (again) the following command:
$ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr.
It still generates the same error as above. Please help
Please provide your .mdp file and topology, if it is small enough to paste into
an email.
-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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