Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups
> 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) Read closely - "T-Coupling group", not "group". You choose the T-Coupling groups from among those in the .ndx file (or from the default groups in its absence, as you're doing here) and specify them in the .mdp file. Thus you should look there first of all. You need to use a disjoint set of T-Coupling groups, so this error is consistent with not having done that. If you were using .ndx file (which you aren't), it might be possible your .ndx file doesn't correspond to your post-genion structure and something weird happens. I'd expect GROMACS woud die with a more helpful error in such a case though. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups
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? 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. -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genion causing atom to be in multiple T-Coupling groups
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
.top before:
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound#mols
Protein_E 1
Protein_I1
Protein_A 1
SOL 9719
.top after
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound#mols
Protein_E 1
Protein_I1
Protein_A 1
SOL 9716
CL-3
These are my commands:
#
#Run grompp
#
emfile_mdpfile='em.mdp'
emout='em_out.mdp'
structure_file='em.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)
#
#Run genion
#
ion_out='ion.gro'
os.system('/usr/local/bin/genion -s '+structure_file+ ' -o '
+ion_out+ ' -nname Cl -nn 3')
#
#Run grompp
#
structure_file_after_genion='em_genion.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p '
+topologyfile)
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[gmx-users] genion causing atom to be in multiple T-Coupling groups
Dear Users,
I'm trying to neutralize my system adding 3 Cl ions with genion and when
running grompp again 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! So there is 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.
_*
*_Best regards for any help, Una Bjarnadottir
_*
.top before:
*_; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound#mols
Protein_E 1
Protein_I1
Protein_A 1
SOL 9719
_*.top after*_
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound#mols
Protein_E 1
Protein_I1
Protein_A 1
SOL 9716
CL-3
_*These are my commands:*_
#
#Run grompp
#
emfile_mdpfile='em.mdp'
emout='em_out.mdp'
structure_file='em.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)
#
#Run genion
#
ion_out='ion.gro'
os.system('/usr/local/bin/genion -s '+structure_file+ ' -o '
+ion_out+ ' -nname Cl -nn 3')
#
#Run grompp
#
structure_file_after_genion='em_genion.tpr'
os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po '
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p '
+topologyfile)
___
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