On 12/30/17 11:44 PM, Neha Gupta wrote:
At first, I gave,
gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc
I selected "system" for output
It says
Program gmx trjconv, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c,
lin
At first, I gave,
gmx trjconv -pbc whole -s prd.tpr -f prd.xtc -o trajwhole.xtc
I selected "system" for output
It says
Program gmx trjconv, VERSION 5.1.4
Source code file:
/cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/gmx_trjconv.c,
line: 1322
Fatal error:
Index[6376] 6377 is lar
On 12/30/17 10:47 AM, Alexandr Nasedkin wrote:
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc
-n index.ndx -center
Removing jumps and centering simultaneously should be considered
mutually exclusive. One usually needs a few rounds of trjconv, e.g.
gmx trjconv -pbc w
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n
index.ndx -center
Please read this first:
http://manual.gromacs.org/documentation/2016.1/onlinehelp/gmx-trjconv.html
trjconv is quite powerful, so it worth to know available options.
-Alexandr
On 30/12/2017 16:37, Neha G
Hi Justin,
Can you please let me know the exact commands?
None of the commands which I tried are working...
Thanks,
Neha
On Thu, Dec 28, 2017 at 7:04 PM, Justin Lemkul wrote:
>
>
> On 12/28/17 8:33 AM, Neha Gupta wrote:
>
>> Hi,
>>
>> I tried this one
>>
>> gmx trjconv -s prd.tpr -f trajwh
On 12/28/17 8:33 AM, Neha Gupta wrote:
Hi,
I tried this one
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
index.ndx
This asks me to select a group fro clustering and then select a group for
output..
What should I select first and then next?
Clustering isn't rele
Hi,
I tried this one
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
index.ndx
This asks me to select a group fro clustering and then select a group for
output..
What should I select first and then next?
Thanks,
Neha
On Thu, Dec 28, 2017 at 5:44 PM, Lakshman Ji Verma
Do it multiple times by center the ligand first and then protein in the
other step,while using pbc. Use -pbc mol option in one of the step to get
the whole molecule.
Thanks
On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta wrote:
> I gave
>
> gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -
On 12/28/17 6:25 AM, Neha Gupta wrote:
I gave
gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o
PRD.pdb
Is there any other alternate command?
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
-Justin
Thanks,
N
I gave
gmx trjconv -pbc nojump -s prd.gro -f prd.xtc -e 5.0 -n index.ndx -o
PRD.pdb
Is there any other alternate command?
Thanks,
Neha
On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH
wrote:
> Hi,
>
> migh be visualization error
>
> Apply pbc
>
> On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupt
Hi,
migh be visualization error
Apply pbc
On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta
wrote:
> Hi,
>
> I tried running the simulations for 50 ns.
>
> The protein breaks (but ligand remains in the active site of the protein
> and it is stable throughout )
>
> How to fix it?
>
> Thanks,
> Neha
Hi,
I tried running the simulations for 50 ns.
The protein breaks (but ligand remains in the active site of the protein
and it is stable throughout )
How to fix it?
Thanks,
Neha
On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:
> Depends. If you're interes
Depends. If you're interested in local folding and there are SS motifs in
the region you're interested, then yes. If not, no. In terms of overall
folding of the entire protein, yes it surely can be an important analysis.
J
On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta wrote:
> Thank you Joao and
Thank you Joao and Aman.
I have noted the points you have suggested.
Do you think analyzing DSSP would help?
Thanks,
Neha
On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:
> "You can use various supporting tools from R language to debug your
> trajectory bu
"You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory"
What? How is this useful or helpful? At most it c
You can try rmsd and gyrate plot to see the changes in your complex. It
On Dec 19, 2017 2:22 PM, "RAHUL SURESH" wrote:
> Also you must know, a lot analysis are available over the entire manual of
> Gromacs where all cannot be performed. Gromacs always provide you all
> necessary analysis but to c
Ok..Thank you..
I'll extend my simulation upto 50 ns.
Thanks,
Neha
On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli wrote:
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> mostly, NO
>
> Search what time range 'protein folding' is happening.
>
> How to
Also you must know, a lot analysis are available over the entire manual of
Gromacs where all cannot be performed. Gromacs always provide you all
necessary analysis but to choose which one is always your choice that suits
your simulation purpose.
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote:
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote:
> Hi,
>
>
> Thank you for your prompt reply.
>
> By clustering analysis, are you talking about gmx cluster command?
>
> "over particular PC sub space"
>
> Could you please elaborate a bit?
Yea clustering analysis can interpret a lot datas about
Hi,
Thank you for your prompt reply.
By clustering analysis, are you talking about gmx cluster command?
"over particular PC sub space"
Could you please elaborate a bit?
Thanks a lot once again.
Thanks,
Neha
On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH
wrote:
> On Tue, 19 Dec 2017 at 12:3
On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote:
> Hi gromacs users,
>
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> How to do it?
>
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
>
> W
On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta wrote:
> Hi gromacs users,
>
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm fo
After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?
mostly, NO
Search what time range 'protein folding' is happening.
How to do it?
I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?
You might want to do P
Hi gromacs users,
After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?
How to do it?
I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?
We observe hydrogen bonds through molecular docking. Hence, I want to ma
Yes, you can open all structural output files with VMD. Or Chimera (tools MD so
on).
On Thursday, April 6, 2017 9:56 AM, Neha Gupta
wrote:
Hi gromacs users,
I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).
I want to know whether there i
Hi gromacs users,
I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).
I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulati
Hi gromacs users,
What are the steps for simulation to observe protein folding in gromacs?
Thanks,
Subashini.K
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org
27 matches
Mail list logo
