Dear users,
I used g_mdmap to calculate the C-alpha contact map of
the trajectory. the distance cut off of 8.0 Ang was selected
The protein is a dimer of 237 residues. The output of -no was
like this -
#resratio tot mean natm mean/atm
1 1.000 473 473.0001 473.000
2
Here's the complete log file:
https://dl.dropbox.com/u/11027999/make.log
Thanks in advance.
Fernando.
On Jan 31, 2013, at 10:05 PM, Roland Schulz wrote:
> On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela
> wrote:
>
>> Dear Gromacs users,
>>
>> I'm trying to install GMX 4.6 in a 64 Bit Machin
On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela
wrote:
> Dear Gromacs users,
>
> I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680
> cards, I've already installed the intel compilers, cuda 5 and openmpi.
>
> I do the following procedure:
> CC=/opt/intel/bin/icc CXX=/opt/intel/
Dear Gromacs users,
I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680 cards,
I've already installed the intel compilers, cuda 5 and openmpi.
I do the following procedure:
CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake ..
then
sudo make -j 12
and I get this error:
Li
On 1/31/13 6:17 PM, S. Alireza Bagherzadeh wrote:
--
Message: 1
Date: Thu, 31 Jan 2013 16:57:56 -0500
From: Justin Lemkul
Subject: Re: [gmx-users] Re: Inquiry about a completely user defined
force field
To: Discus
On 1/31/13 5:09 PM, FX wrote:
It would be useful to see the .n2t file and the screen output about what's
problematic. g_x2top cannot identify suitable entries in the .n2t file for 36
of your atoms, so some combination of atoms is not accounted for, either by
omission in the .n2t file or fro
> try acpype iso g_x2top (this comes straight from the developer).
Two questions:
1. How's that supposed to work? I tried, it doesn't work, acpype does not
know "iso" or "g_x2top" arguments
2. I'm not using AMBER as forcefield, so I'm not sure if that wrapper on
ambertools is appropriate
T
> It would be useful to see the .n2t file and the screen output about what's
> problematic. g_x2top cannot identify suitable entries in the .n2t file for
> 36 of your atoms, so some combination of atoms is not accounted for, either
> by omission in the .n2t file or from a configuration that doe
On 2013-01-31 22:55, FX wrote:
Hey Matt,
(It's a small world, eh?)
I don't have a particular reason to use Gromacs. I used it for small ions
solvation ten years back, I liked it, but every time I have tried to use it
since for crystalline systems, I was put off because, as you say, it's proba
On 1/31/13 11:53 AM, George Patargias wrote:
Dear Gromacs list
I would like to ask a question regarding the global rotation and
translation removal in GROMACS.
In my mdp file I use the following options:
; mode for center of mass motion removal
comm-mode= Linear
; number of st
On 1/31/13 1:57 PM, S. Alireza Bagherzadeh wrote:
Dear Dr.Abraham,
Thank you for taking the time to look at my files.
However, I have one question remained in my mind:
Where is the "atomtypes.atp" used in the force field?
I suspect that this file is only for clarification for the user in
ord
Hey Matt,
(It's a small world, eh?)
I don't have a particular reason to use Gromacs. I used it for small ions
solvation ten years back, I liked it, but every time I have tried to use it
since for crystalline systems, I was put off because, as you say, it's probably
not what it's designed for.
On 1/31/13 4:10 PM, Matt Watkins wrote:
Oops. Well, I'd be interested in people's opinions and don't intend to hijack
FX's thread.
I do use the code regularly and greatly appreciate all the effort that people
have put into its development. But, particularly, the inability to easily mix
bucking
On 1/31/13 2:32 PM, FX wrote:
Hello,
I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one
big molecule extending throughout space with PBC. I have prepared my .gro file
from the PDB (and checked it with babel/vmd). I'm trying to generate the
topology with g_x2top.
Oops. Well, I'd be interested in people's opinions and don't intend to
hijack FX's thread.
I do use the code regularly and greatly appreciate all the effort that
people have put into its development. But, particularly, the inability to
easily mix buckingham and lennard-jones is awkward for
Hey FX,
out of interest (and I ask off list as it is probably not very politically
correct) why do you want to use gromacs? I've found it to be a nightmare
for other than proteins/trivial systems.
Hope things are well,
Matt
On Thu, 31 Jan 2013 19:32:36 -, FX wrote:
Hello,
I'm tryi
Hello,
I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one
big molecule extending throughout space with PBC. I have prepared my .gro file
from the PDB (and checked it with babel/vmd). I'm trying to generate the
topology with g_x2top. I have:
- created a directory
Hello,
I would like to know if it's possible to give a specific name to an hydrogen
which will be added thanks to the .hdb file.
Indeed, by default, the hydrogens added on the same carbon have the same
name with the last number incremented by 1.
Example : for charmm36, the hydrogens added to th
Dear Gromacs list
I would like to ask a question regarding the global rotation and
translation removal in GROMACS.
In my mdp file I use the following options:
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm
On 2013-01-30 23:48, Ricardo Soares wrote:
Hello,
before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, eve
On 1/31/13 9:51 AM, az kalsom wrote:
hi
i have docked the compund with protein and selected the best protein-ligand
conformation for simulations,
but when i generate the topolgy for ligand by
Automated Topology Builder (ATB) and Repository , job is killed every tym.
error message is 1) geomet
On 1/31/13 3:19 AM, Najmeh Fani wrote:
Hello
please help me I have a question
in gpcr tutorial when I run energy minimization process for inflategro with
this command:
grompp -f EM.mdp -c system_inflated.gro -p topol.top -o EM.tpr -maxwarn 5
I seen an error :
Fatal error:
[ file strong_posre.
Hello
please help me I have a question
in gpcr tutorial when I run energy minimization process for inflategro with
this command:
grompp -f EM.mdp -c system_inflated.gro -p topol.top -o EM.tpr -maxwarn 5
I seen an error :
Fatal error:
[ file strong_posre.itp, line 57 ]:
Atom index (53) in position_
23 matches
Mail list logo
