Tsjerk and Justin thanks for your suggestions.
Justin, the combination you suggested did not work, I tried many things
without succes here.
I got the following error using whole and mol. (after doing nojump)
There were 8 inconsistent shifts. Check your topology
There were 8 inconsistent shifts. Check your topology
Will stop reporting inconsistent shifts
Tsjerk you are right I should explain the names:
trjconv -f gromacs.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
top140.tpr
gromacs.trr = trajectory generated by replica exchange
cluster.trr = output name
lig_prot.ndx=index file of with a group for ligand and protein
top140.tpr=tpr file generated using the starting configuration of
gromacs.trr
You were right about the fit last time, but the error stays the same if I
don't do the fit first...
Could the it be the fact that it is a replica exchange simulation that
causes the problem, this makes that there are jumps in the trajectory of
course...
kind regards,
servaas
servaas michielssens wrote:
Dear gromacs users,
I have a problem that is already discussed a lot on the mailing list,
in a protein-ligand simulation the ligad jumps out of the box. The
trajectory is generated by replica exchange simulation. So I used
trjconv with the option cluster:
trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
top140.tpr
The program seems to get stuck at frame 208, repeating the following
lines:
COM: 1.730 1.730 2.447 iter = 6214 Isq = 21.428
COM: 0.000 0.000 0.000 iter = 6215 Isq = 54.757
COM: 1.730 1.730 2.447 iter = 6208 Isq = 21.428
COM: 0.000 0.000 0.000 iter = 6209 Isq = 54.757
COM: 1.730 1.730 2.447 iter = 6210 Isq = 21.428
COM: 0.000 0.000 0.000 iter = 6211 Isq = 54.757
COM: 1.730 1.730 2.447 iter = 6212 Isq = 21.428
if I use this command:
trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster
The program runs but the ligands is still out of the box, the option
-s seems to be necessary, but not working in my case.
I also tried the -nojump option and after this the whole option but in
visualistion (with VMD) I got strange bonds...
I've found that sometimes several iterations of trjconv are necessary to
get such things fixed up. Something like -pbc nojump, followed by
'whole,' and 'mol' or 'res' after that might do the trick. It's a bit
of trial and error, and if anyone else out there has a better method,
I'd love to hear it, too :-)
-Justin
An often reported problem was that the the structure in the tpr file
is not close enough to the starting structure in the trajectory, I
tried it by making a tpr file with a the strating structure of the
trajectory (in this structure the ligand is in the active site if I
look at the structure). But this did not help.
What I am doing wrong here?
thanks in advance for your help!
kind regards,
servaas
_______________________________________________
Hi Servaas,
trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
top140.tpr
I think there's quite a bit of reason to start calling you names here :)
Assumedly, fit.trr means that it results from fitting the trajectory
to a reference?
So what does this do with your PBC?
I also tried the -nojump option and after this the whole option but in
visualistion (with VMD) I got strange bonds...
Right, so strange bonds should be quite an indication that there's
something weird with your shifts.
An often reported problem was that the the structure in the tpr file is
not
close enough to the starting structure in the trajectory, I tried it by
making a tpr file with a the strating structure of the trajectory (in
this
structure the ligand is in the active site if I look at the structure).
But
this did not help.
Another often, or at least several times, mentioned problem relates to
the fact that fitting a structure reorients the molecule, but leaves
the PBC as it is, causing a mismatch between the system and the PBC.
Therefore one can not execute any PBC related operations (nojump,
cluster, whole), after the trajectory has been fitted.
No hard feelings ;)
Cheers,
Tsjerk
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
