On 9/22/12 10:04 PM, Leandro Bortot wrote:
Dear all,
I am trying to do a glycoprotein simulation with GROMACS using the
AMBER99SB-ILDN forcefield together with GLYCAM06.
After constructing my glycoprotein grompp gives the following warning
for most of the atomtypes defined in the .itp file with the glycoprotein
parameters:
WARNING 23 [file glycoprot.itp, line 27]:
Overriding atomtype CC
Is this supposed to be this way?
Because there are new definitions of atomtypes which are not used in
the carbohydrate nor in the glycosylated residue, I suppose that these
parameters are really meant to override the default ones since they are
only necessary for water and ions. Am I right?
An atom type of "CC" is certainly nothing to do with water and ions - it's a
carbon atom type. Above you say the warnings are generated from the
glycoprotein topology. That's your problem. The parameters introduced here are
fighting those built into the AMBER99SB-ILDN force field. Atom types are
case-sensitive, so if you truly need new parameters then you can change the case
and they will not override. If the atom type parameters are duplicates of
existing ones, then you can ignore the warning.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
