Among other places, there was a thread here two days ago with that title
;-)
On Mar 23, 2014 3:34 AM, "Christopher Neale"
wrote:
> where do you learn this stuff ? ;)
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun
Dear Users
I am trying to run a drug-protein simulation in GROMACS. I have calculated
the ligand paramteres using the generalized amber force field (GAFF) . ESP
partial charges were calculated using HF/6-31G* basis set. RESP fitting was
performed using the Antechamber . Now I am having trouble in
where do you learn this stuff ? ;)
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 22 March 2014 21:50
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1
On 3/22/1
On 3/22/14, 9:13 PM, Collins Nganou wrote:
Dear Users,
I am unable to generate the file.gro with gromacs.4.6.3-1.
However, I have obtained the file.top after using
pdb2gmx -f TTb.pdb -o TT.gro -p TT.top -ignh
...
This appears after I have change the version of gromacs from 4.5-4 to
4.6.3-
On 3/22/14, 3:39 PM, GtrAngus wrote:
Hi there,
I am trying to simulate a membrane but for now I kept it simple and I just
have a box full of water. Now I want to calculate the polarisation density P
= Q * R. Q is the charge and R the distance between two atoms in a molecule
(here O-H ).
Getti
On 3/22/14, 7:41 PM, shivangi nangia wrote:
Hello All,
I have a question regarding case sensitivity for index file group names.
If I have a group named "l"ipid (i.e. lipid) in the index file but I have
it as "L"ipid (i.e. Lipid) in the .mdp file, does that matter?
I am not getting any errors
Dear Gromacs Users,
My system consist of a proteins ( membrane channel) and a drug (DOX)
and i am trying to run a pull_md in order to force the drug to permeate the
channel, but,
the channel size and the durg molecule are closed, so i've been reading , i
dont know if i should use constraint to
If you want only the .gro file, then you don't need to run pdb2gmx. Try
editconf -f my.pdb -o my.gro .
If your running pdb2gmx to get the .top file (the reason why pdb2gmx exists,
although I agree that the program name is commonly confusing), then I can't
help you much since that error message
Dear Users,
I am unable to generate the file.gro with gromacs.4.6.3-1.
However, I have obtained the file.top after using
pdb2gmx -f TTb.pdb -o TT.gro -p TT.top -ignh
...
This appears after I have change the version of gromacs from 4.5-4 to
4.6.3-1
I am not able to find any error in the output.
Hi,
All you need is in the hbm and hbn output.
Best regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Associate
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 22 Mar 2014, at 07:08, pratibha wrote:
> Hi all,
>
Hello All,
I have a question regarding case sensitivity for index file group names.
If I have a group named "l"ipid (i.e. lipid) in the index file but I have
it as "L"ipid (i.e. Lipid) in the .mdp file, does that matter?
I am not getting any errors while running any gmx command but I feel my
sys
Hi pratibha,
in my opinion, you have 2 choices:
1.) You use VMD and switch the view to hydrogen-bonds. There are different
options to do so, but afaik it is always 3D.
2.) You make your own C/C++-Code. But of course, this is much more work to
do :)
I guess it depends what you wanna do? Just for
Hi there,
I am trying to simulate a membrane but for now I kept it simple and I just
have a box full of water. Now I want to calculate the polarisation density P
= Q * R. Q is the charge and R the distance between two atoms in a molecule
(here O-H ).
Getting the distances is fine but I had troubl
Hi all,
I would like to create 2D probability density map of backbone hydrogen bonds
between two peptide residues. Is it possible to do so using gromacs?
I have read that g_mdmat makes distance matrices consisting of the smallest
distance between residue pairs. Is it possible to use such a tool t
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