> Is the problem specific to cylinder geometry? Do other settings work? Does
> it
> make a difference if you set values for pull_r0 and pull_r1?
>
> -Justin
I would think that it is the cylinder geometry that creates the problem.
If I use
pull= umbrellapull_geometry
I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb
The main problem is: When I use pdb2gmx it adds H atoms to Cys,
hence the disulfide bonds are no longer conected after energy minimization.
How can I avoid this addition of H atoms?
(I tried to make this bond after, but
On 29/04/2012 7:02 PM, Hagit G wrote:
I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb
The main problem is: When I use pdb2gmx it adds H atoms to Cys,
hence the disulfide bonds are no longer conected after energy minimization.
How can I avoid this addition of H atom
Actually, I am confused somehow.
I want to equilibrate the system. It contains popc and water. To equilibrate
it, using .mdp file I use the nvt.mdp file as below.
title = NVT equilibration for POPC
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator
On 29/04/2012 7:32 PM, Shima Arasteh wrote:
Actually, I am confused somehow.
I want to equilibrate the system. It contains popc and water. To
equilibrate it, using .mdp file I use the nvt.mdp file as below.
title= NVT equilibration for POPC
define= -DPOSRES; position restra
Dear MArkWow, That was kind of you.
I appreciate you.
Ok, I will try it.
Thanks,
Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Sunday, April 29, 2012 2:11 PM
Subject: Re: [gmx-users] Make an index file
On 29/04/2012 7:32 PM, Shima Ar
thank you very much
That was what I've tried to use "pdb2gmx-ss", this is not useful,
'cause it's not in the same unit.
My problem is not the distance.
Hagit
2012/4/29, Mark Abraham :
> On 29/04/2012 7:02 PM, Hagit G wrote:
>> I'm trying to work on thrombin pdf file with 2 chains. The pdb co
Dear Mark,
Wow, That was kind of you.
I appreciate you.
Ok, I will try it.
Thanks,Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Sunday, April 29, 2012 2:11 PM
Subject: Re: [gmx-users] Make an index file
On 29/04/2012 7:32 PM, Shima Ar
On 4/29/12 4:46 AM, J B wrote:
> Is the problem specific to cylinder geometry? Do other settings work? Does it
> make a difference if you set values for pull_r0 and pull_r1?
>
> -Justin
I would think that it is the cylinder geometry that creates the problem.
If I use
pull = umbrella
pull
> Does the cylinder geometry work if you use "pull_start = no" and pull_init1
> equal to your starting (restraint) distance? I'm just trying to go through
> all
> of the iterations of what might be failing. In theory, what you're doing is
> fine but I'd be interested to know if there was som
I have sent this email to the gromacs users emailing list.
I don't actually use g_spatial as it doesn't do what I want it to, I use the
older g_sdf script. So can't comment on the output or really help you with it.
What you are doing seems right from a quick look through. From what you have
t
I have posted this to the gromacs users emailing list.
No files came through, generally they are stripped off the emails before being
posted to the emailing list. Should never send attachments to an emailing
list, post them to the internet and put the URLs in the email for people to
look at if
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung wrote:
> Hi,
>
> Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you
> know, automatic threading is awesome because it allows me to start parallel
> runs without calling mpirun. So on version 4.5.5, I can start a job on
> eight
On 30/04/2012 3:38 PM, Anirban Ghosh wrote:
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung
mailto:adeyo...@andrew.cmu.edu>> wrote:
Hi,
Typically, I use Gromacs 4.5.5 compiled with automatic threading.
As you
know, automatic threading is awesome because it allows me to star
Respected Sir,
While i am running the gromacs software to simulate
the protein i am getting the following error.
Fatal error:
Residue 'GNP' not found in residue topology database
Suryanarayna Seera,
PhD student.
--
gmx-users mailing listgmx-users@gromacs.org
http://l
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana
wrote:
> Respected Sir,
>
> While i am running the gromacs software to simulate
> the protein i am getting the following error.
>
> Fatal error:
> Residue 'GNP' not found in residue topology database
>
>
http://www.gromac
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