Dear Justin
Thank you very muchh
Sogol
From: Justin A. Lemkul
To: Kowsar Bagherzadeh ; Discussion list for GROMACS
users
Sent: Thursday, May 24, 2012 9:59 AM
Subject: Re: [gmx-users] g_rms -bm
On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:
>
>
> Dear U
On 5/24/12 8:19 AM, rama david wrote:
Thank you for your reply,
I am asking you again same question, EXTREMELY SORRY for my stupidity,
In step six , I unable to differentiate npt and production run by
mdp file as usualy we find difference by define term,
I think I get meaning upto reason why
Thank you Justin for these correct explanation
Its really clear my lot of queries..
> For the tutorial, NPT is conducted with restraints on all protein heavy
> atoms. The production runs are conducted by restraining only one chain for
> practical reasons.
>
> These is my question ;
>
If we are
Dear Gmx Users,
I want use distance restraints of 3 atoms belonging to 3 different
moleculetypes. In this case shall I create and index file of those atoms
and then use:
genrestr -f X.pdb -n index.ndx -disre -o disre.itp ?
Under which topology file shall I add:
#ifdef DISRES
# include 'disre.it
Hello. Is it possible to perform MD for protein-ligand interactions in
implicit water? And what about the precision of this kind of MD's? Are
they differ strong from these with explicit water?
--
Andrew Gontchar
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Hi Gromacs users,
I have a problem getting a snapshots using trjconv. If you could help me, I
would be very grateful. Below, I try to explain what I did and problem
happened.
Firstly, I have done 10ns long simulation (several peptides in a box). And
then, using the outputs of that simulation (conf
On Thu, May 24, 2012 at 5:24 PM, Turgay Cakmak wrote:
>
> Hi Gromacs users,
>
> I have a problem getting a snapshots using trjconv. If you could help me,
> I would be very grateful. Below, I try to explain what I did and problem
> happened.
> Firstly, I have done 10ns long simulation (several pept
Hi Rama,
Thanks for your quick reply.
Catenate two trajectory with help of trjcat -h
to get snapshot of particular time use trjconv -dump
use appropriate pbc option
I have also used trjconv with -dump and -pbc nojump options, but still I
have same problem.
you are using -b 1 -e 1
mean
Hi ,
You run extended simulation of 10 ns on your first 10ns simulation .
You get traj20ns.xtc.
these new trajectory contain all the tme frame from onwards 10ns.
So if you are giving command
trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
snapshot20ns.gro (Note: traj20ns.xtc is n
Dear Gmx Users,
I want to use distance restraints of 3 atoms which belong to 3 different
proteins. For this purpose I want to create one topology so one
moleculetype:
I tried to use pdb2gmx -chainsep ter (where i put TER after each chain in
my PDB)
But 3 separate topologies were created.
I want
On Thu, May 24, 2012 at 3:42 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I want to use distance restraints of 3 atoms which belong to 3 different
> proteins. For this purpose I want to create one topology so one
> moleculetype:
>
> I tried to use pdb2gmx -chainsep ter (where i put TER after ea
Dear gmx users,
ACE is defined in CHARMM-27 .rtp file, but I don't see this residue in
CHARMM-36 .rtp file . Is it OK, if I add the ACE from CHARMM-27 into CHARMM-36?
And use the CHARMM-27 [ACE] parameters in CHARMM-36?
Thanks in advance.
Sincerely,
Shima--
gmx-users mailing listgmx-use
Hi Steven,
Doesn't -chainsep take an argument?
Cheers,
Tsjerk
On May 24, 2012 5:33 PM, "Steven Neumann" wrote:
On Thu, May 24, 2012 at 3:42 PM, Steven Neumann
wrote: > > Dear Gmx Users,...
It is stated:
The separation of chains is not entirely trivial since the markup in
user-generated PDB
Hello
I want to equilibrate the water around my molecule. For doing this I created a
pr.mdp file that makes most sense for me. Sadly I am a beginner with less
knowledge, so could you please take a look on this pr.mdp file and say me if
this is good or if not, what would you suggest to me? My Sy
Hi all,
I am trying to minimize a system containing DNA+protein, I just want
to energy minimize hydrogen atoms for 500 steps , while the rest of the
structure is kept fixed. How can i do it in gromacs. Please suggest me a way.
Thank you
On Thu, May 24, 2012 at 6:05 PM, Tsjerk Wassenaar wrote:
> Hi Steven,
>
> Doesn't -chainsep take an argument?
>
> Cheers,
>
> Tsjerk
>
It does, I used option: -chainsep ter
And I had in my pdb file after each chain TER and thus 3 itp files were
created corresponding to my top file and representi
http://tgiturkiye.net/breakingnews/63LeePhillips/";>http://tgiturkiye.net/breakingnews/63LeePhillips/
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Hi Steven,
So it did what you told it to do. You want -chainsep no or none. Doing
it from the top of my head, so I'm not sure. But it'll be listed in
the help what options there are.
Cheers,
Tsjerk
On Thu, May 24, 2012 at 8:29 PM, Steven Neumann wrote:
>
>
> On Thu, May 24, 2012 at 6:05 PM, Ts
I had the same problem and I didn't find any way to do it. So i created new
residues for the terminals, and I added them to the forcefields files.
Example: if my first COOH terminal was a SER i created a SERT residues and I
used the COOH values taken from ASP , and the same procedure was used for
Okay,okay, I give in. To settle this again, I looked it up, and among
the options to -chainsep is 'interactive'. If you use that you're
prompted whether or not to separate at the breaks pdb2gmx detects.
That allows you to merge chains. I guess there'd be sense in just
having an option 'no' to merge
Tahnk you both. Indeed, it works so -chainsep interactive
Steven
On Thu, May 24, 2012 at 9:44 PM, Tsjerk Wassenaar wrote:
> Okay,okay, I give in. To settle this again, I looked it up, and among
> the options to -chainsep is 'interactive'. If you use that you're
> prompted whether or not to sepa
I checked and the resul is the same...but now I know I can use -chainsep
interactive!
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Sure, CHARMM 36 is just a modification to the lipids. The protein (and other
sutff) parameters are untouched.
regards
Felipe
Mensaje original De: shima_arasteh2...@yahoo.com Fecha: 24-may-2012
12:41 Para: "Discussion list for GROMACS users" Asunto:
[gmx-users] CHARMM-27 & CHARMM
Dear Users:
Summary:
I believe that there is some problem in the residue numbering routine that is
used by editconf and trjconv
that exists at least in 4.5.3 and 4.5.5, but not in 4.0.7, and that this is
somehow related to the ACE residue.
Details:
I have a system with two peptides, water, and
On 5/24/12 6:35 AM, rama david wrote:
Thank you Justin for these correct explanation
Its really clear my lot of queries..
For the tutorial, NPT is conducted with restraints on all protein heavy
atoms. The production runs are conducted by restraining only one chain for
practical re
On 5/24/12 10:17 AM, rama david wrote:
Hi ,
You run extended simulation of 10 ns on your first 10ns simulation .
You get traj20ns.xtc.
these new trajectory contain all the tme frame from onwards 10ns.
So if you are giving command
trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
sna
On 5/24/12 2:19 PM, Kartheek wrote:
Hi all,
I am trying to minimize a system containing DNA+protein, I just
want to energy minimize hydrogen atoms for 500 steps , while the rest of the
structure is kept fixed. How can i do it in gromacs. Please suggest me a way.
Have a look
On 5/24/12 1:58 PM, Lara Bunte wrote:
Hello
I want to equilibrate the water around my molecule. For doing this I created a
pr.mdp file that makes most sense for me. Sadly I am a beginner with less
knowledge, so could you please take a look on this pr.mdp file and say me if
this is good or i
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