On 5/1/12 4:12 PM, Lara Bunte wrote:
Hi Justin
Thanks, that makes sense. I have the group "Close to ISO" that contains the
water molecules in my specified region and I have the group ISO and therefore the next
step is to unite this two groups.
If I typed
make_ndx -f molecule.pdb -n index.ndx -o index_new.ndx
the make_ndx program shows only one group, the "Close to ISO" with number 0 and
no other groups, so how to merge them?
I typed l for "list residues" and than there was ISO and SOL.
Now if I am at this place, how to tell GROMACS, that ISO is a group also, that I can
merge it with "Close to ISO"?
My recollection of this feature was wrong; sorry. I assumed the default groups
would be appended to your custom index group, which is not the case.
Create a new index group with:
make_ndx -f molecule.pdb -o index2.ndx
This will contain groups like ISO and SOL. Then just concatenate the existing
index groups:
cat index2.ndx index.ndx > index3.ndx
Then attempt to do what I said before, operating with index3.ndx, i.e.:
make_ndx -f molecule.pdb -n index3.ndx -o index_final.ndx
where index_final.ndx will have the merged groups.
-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
========================================
--
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
