On 5/22/17 4:04 AM, abhisek Mondal wrote:
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) a
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate
Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it.
On 5/21/17 9:47 AM, abhisek Mondal wrote:
I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.
However, when I tried to reapply the same code (with modified COMs and thus
pu
I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.
However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, somethin
On 5/19/17 5:56 AM, abhisek Mondal wrote:
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
On 5/17/17 8:55 AM, abhisek Mondal wrote:
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Def
On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote:
>
>
> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
>> This time I think I got ligand restrained successfully during the umbrella
>> sampling. I have removed the restrain from protein, as per your advice.
>> Defined the COM vector in md_umbrella
On 5/17/17 8:55 AM, abhisek Mondal wrote:
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded t
This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in t
On 5/15/17 2:45 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
On 5/11/17 9:21 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having m
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in thi
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul wrote:
>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in thi
On 5/11/17 1:25 PM, abhisek Mondal wrote:
Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.
One thing I'm worried
Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.
One thing I'm worried about here. In previous mail, I mentioned the
On 5/11/17 9:21 AM, abhisek Mondal wrote:
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrel
On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal
wrote:
> Hi,
>
> Thank you for the explanation. It really cleared some concepts. But I'm
> still having my ligand moving in this step. I have modified the code as:
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> p
Hi,
Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pu
On 5/8/17 10:00 AM, abhisek Mondal wrote:
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
On 5/7/17 1:57 AM, abhisek Mondal wrote:
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
foll
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
>
>
> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>
>> Hi,
>>
>> For your ease of understanding regarding what is happening during this
>> above said umbrella-mdrun, I have shared the trajectory video file the
>> following link.
>> https://drive.
On 5/7/17 2:22 PM, abhisek Mondal wrote:
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't mo
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't move this
way.
You mentioned that during this r
On 5/7/17 1:57 AM, abhisek Mondal wrote:
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
Is this normal given t
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
Is this normal given that the mdp code being used ? I basically hav
Hi,
I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
The gro file generated at the end shows the ligand is wa
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