On 27/02/2012 8:35 PM, James Starlight wrote:
Mark,
I've found a possible sollution to restrict oxygens of my X-ray water
by possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
#include "XW.itp"
; Include Position restraint file
#ifdef POSRES_XW
Mark,
I've found a possible sollution to restrict oxygens of my X-ray water by
possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
#include "XW.itp"
; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
; i funct fcx
On 27/02/2012 5:03 PM, James Starlight wrote:
Justin,
2012/2/25 Justin A. Lemkul mailto:jalem...@vt.edu>>
You likely have a [settles] directive applied the the XW molecules
(crystal waters, yes?) and SOL. You can't do that. The block of
molecules to which [settles] are applied
Justin,
2012/2/25 Justin A. Lemkul
>
>
>
> You likely have a [settles] directive applied the the XW molecules
> (crystal waters, yes?) and SOL. You can't do that. The block of molecules
> to which [settles] are applied must be continuous. You'll have to replace
> the [settles] directive in XW
James Starlight wrote:
Today I've tried to model internal water and forced with some problems :)
I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions
1) But when I've m
Today I've tried to model internal water and forced with some problems :)
I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions
1) But when I've made my complete system ( with
On 25/02/2012 5:37 AM, James Starlight wrote:
Mark,
So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to
avoid those sterric issues doesn't it ?
Yes. This was one of the options I suggested earlier.
Wh
Mark,
So as I understood the ussage of X-ray structure as the starting model
where the internal water is already present might be good in case to avoid
those sterric issues doesn't it ?
What are additional options should I use for preparation of such system
with pdb2gmx ? Should I use posres on
On 24/02/2012 6:55 PM, James Starlight wrote:
Mark,
what about the next sollution
firstly I'll align both of my structures ( x-ray with water and
another my model without water)
than I'll copy aligned water from first structure to my model in the
bottom of the GRO file.
than I'll minimise
Mark,
what about the next sollution
firstly I'll align both of my structures ( x-ray with water and another my
model without water)
than I'll copy aligned water from first structure to my model in the bottom
of the GRO file.
than I'll minimise this editted structure to relax side chains of the
On 24/02/2012 6:31 PM, James Starlight wrote:
Up! :)
Please provide me with the best sollution of my problem! I just want
to copy some water mollecules from X-ray structure to my model and
place it in the identical possitions inside the TM budle of my
protein. What are the most trivial way t
Up! :)
Please provide me with the best sollution of my problem! I just want to
copy some water mollecules from X-ray structure to my model and place it in
the identical possitions inside the TM budle of my protein. What are the
most trivial way to solve this task?
James
2012/2/22 James Starligh
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