Una Bjarnadottir wrote:
Una Bjarnadottir wrote:
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with
the new generated .gro file I get this error:
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which is the last water atom (total in system 33003) and groups 15
and 1 are Cl and protein groups if I on the other hand do not
neutralize the system the run goes fine! When looking into the .ndx
file atom 33000 is in 4 groups; 0 (system), 11 (non-protein), 14
(SOL) and 16 (other). How can I change the group definitions and
make sure the groups do not overlap and to be unique?
It seems to be something wrong with how the genion works for me. I
followed the tutorial and chose the SOL group and water molecules
were replaced by the Cl ions. Than I modifyed the .top file and took
3 sol molecules and added the 3 ions.
Please help because have not been able to fix the problem with
related letters on the subject on the list.
Best regards, Una Bjarnadottir
What do your tcoupl groups look like?
tc-grps':'Protein OTHER CL- ###where I have to call SOL: OTHER
otherwise error
Could it be System SOL?
The number may be confusing, you should subtract one from them when
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T
coupling group.
I made the indes file after running genion using the .gro output file
from genion generating it. Also I thought you would have to subtract
one and it was groups 14 and 0 instead of 15 and 1. How would I have
the ions part of the solvent T coupling group? By modifying the .top
file to [ molecules ]
; Compound #mols
Protein_E 1
Protein_I 1
Protein_A 1
SOL+CL- 9719
and than the tc-grps in the .mdp file accordingly to that. How will I
define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal
error: No such moleculetype SOL+CL- came for both.
Best regards David for your reply, Una David.
in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and
15 is CL-)
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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