James Starlight wrote:
Mark,
I've forced with some problems during MDrun of such system with the two
proteins.
Firstly, after addition of second protein, I've removed all water and
ions and solvated my system with genbox and genion.
Than I've redefined groups of my proteins ( wich are like a_1-4000 and
a_4001-5000 ) in index.ndx file in the separate T_coupl, COM and
energygroups because atom order was perturbed after solvation.
Separate COM motion removal groups are tricky. I'm still not completely clear
on what your system looks like, but if you've got two proteins in two layers of
solvent and you expect one or both of them to move in such a way that they begin
to interact, it may not be appropriate to be using the groups you've shown below.
Than I've minimized my system with the Emtool=500
And what was the exact outcome?
The problems were on the nvt equilibration phase with the posres applied
on the both proteins. I have no errors, notes or warninngs from GROMPP
but when I've started my simulation with MDrun my system was crushed on
the 1st step with the multiple LINKS warnings as well as message that
something wrong with interactions between 1st protein atoms and
surrounded water ( as I've said previously after addition of the second
protein to my system I've resolvated my system again).
Please don't attempt to interpret the error message. Copy and paste the actual
output (not the LINCS warnings themselves, we all know what those look like).
Might my system be not properly minimized or does something wrong else
in addition?
That depends on your answers to the questions posed above. You should also
provide a complete .mdp file. If the system crashes on the very first step,
either minimization was insufficient or your .mdp parameters break the
underlying physical model and cause an immediate collapse.
-Justin
James
31 марта 2012 г. 2:20 пользователь Mark Abraham <[email protected]
<mailto:[email protected]>> написал:
On 31/03/2012 1:00 AM, James Starlight wrote:
Mark,
Also I'd like to know some more about most correct parametrisation
of such new edited system. My new system consist of two proteins (
one- wich was initially and the second small peptide wich I've
docked to the first protein). So now I need to define 2 separate
groups for the below enties of my MD files
|energygrps = Protein peptide
|
tc-grps = Protein_Bilayer SOL_ions_peptide
and finally CoM groups because of the general anisotropy of the membrane
system
comm-grps = Protein_Bilayer SOL_Ions_Peptide
I've made itp file for the peptide via pdb2gmx so in th default definition
both the protein and peptide are the protein enty in the index file.
I've separate both of the protein and peptide by selection of two subsets
of atoms wich represent to the each of that enties.
So finally I have two groups in the index.ndx file
a_1-5000 ( it's protein)
a_9999-10500 (it's peptide)
You can use make_ndx (or a text editor on the .ndx file) to give
them more helpful names.
Does this separation correct in general ? I have some fears because both
protein and peptide consist of the same residue numbers in the GRO file ( e.g
there are 212- lys wich is part of the protein and 212-Pro wich is part of the
peptide ) Might this system be tended to errors?
Residue numbers are largely irrelevant. pdb2gmx and maybe grompp use
them for matching a coordinate file to the .rtp and .top
(respectively), but only really in the sense that the number changes
from one residue to another.
I have no errors during processing of that sustem by grompp as well as md
run. What should I do for such system consisted of two proteins in separate
phases ( membrane-like and water)
?
All seems basically sound.
Mark
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
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 [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
