Dear All,
I installed gromacs-4.5.3 using cygwin on windows 7, following the instructions
on http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO.
However, after installation, when I tried to run gromacs, I couldn't find the
"share" folder in D:/cygwin/usr/local/gromacs. This
Dear All,
I installed the gromacs on Ubuntu, and ran the demo. But every time it produces
an output file, I get this error: "output.pdb2gmx: Permission denied.", so I
can't view the output. I am also unable to locate the .trr file, which is
supposed to be the ultimate output of demo. Could anyo
I have attached the output of demo, and another Okay, I just ran the demo and
kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here
is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx program
Press
St
I have attached the output of "demo", and "water" with the message.
I just ran the demo and kept pressing enter whenever it asked me. Demo ran the
pdb2gmx first, and here is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx pr
Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.
Best,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sun, February 13, 2011 9:30:52 AM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan
Okay, thanks. I will install it again in some other directory.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, February 13, 2011 1:39:16 PM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan wrote:
> Thanks, Justin! Sudo
Dear All,
I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in
my home folder following the instructions on
http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do
"make", I get an error in the end (pasted below). I have also attached the log
package and add it into
repository.
There maybe also some other ways.
HTH,
lina
On Tue, Feb 15, 2011 at 6:23 AM, majid hasan wrote:
Dear All,
>
>I am trying to install gromacs in ubuntu. I configured both fftw and gromacs
>in
>my home folder following the instructions o
?
Best Regards,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Mon, February 14, 2011 6:46:47 PM
Subject: Re: [gmx-users] Gromacs Installation
majid hasan wrote:
> Okay, I'll try with --enable-single. But as far as I unde
Okay. Actually, second time, I over-worte the first installation. I mean I
didn't uninstall the first one, I just ran the whole process again starting
from
fftw$./configure. I am not sure if that is all right, I just did it to find out
the problem. In the third attempt (without issuing --enable
bject: Re: [gmx-users] Gromacs Installation
"clean" reinstallation.
make uninstall
make distclean
rm -r
from source re-install it again.
lina
On Tue, Feb 15, 2011 at 12:39 PM, majid hasan wrote:
Okay. Actually, second time, I over-worte the first installation. I mean I
didn&
, February 14, 2011 9:39:12 PM
Subject: Re: [gmx-users] Gromacs Installation
On 15/02/2011 4:35 PM, majid hasan wrote:
Okay, I'll do this. I have also realized after browsing through
config.log, that Xlib.h is absent. Where do I get it, I want it to
run
ngmx.
>
You w
Dear All,
I want to simulate interaction between single strand dna and cnt. I tried to
use
Biomer (from case group webpage), but it's not working. When I try to open
B.html in my browser, I get a blank page. Could anyone please tell me if there
is another way to generate .pbd file for dna?
Th
Dear All,
I am trying to simulate the interaction between DNA, and CNT. But when I try to
create the toplogy file with command
g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal
error: Could only find a forcefield type for 119 out of 287 atoms
I am using the oplsa
Thanks,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Fri, April 8, 2011 12:54:38 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
> Dear All,
>
> I am trying to simulate the interaction between DNA, and CNT. But when I try
> to
&g
Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
> Thanks Justin!
> But with pdb2gmx, after selecting force field and water model, I get this
>error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting
>oplsaa), and when I selected amber99, I got
bject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
> Okay, I'll try to create a better .pdb file, and see how it goes. So if
> oplsaa
>doesn't have nucleic acids, then Amber is a better choice?
>
A force field should be chosen based on thorough study of the
Oh, yes, I could open it in text editor. I didn't realize that.
Thanks,
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Fri, April 8, 2011 6:48:13 PM
Subject: Re: [gmx-users] .n2t file for ssDNA
majid hasan wrote:
> I looked at
Dear All,
I am trying to make sure that the names of dna residues in my .pdb file match
with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file
(attached), and it gives the names for DNA residues, which are of the form, DX,
DX3, DX5, DXN (X=A,C,T,G). So if I have a residue
Okay, thanks a lot.
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sat, April 9, 2011 3:05:48 PM
Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file
majid hasan wrote:
> Dear All,
>
> I am tryin
Dear All,
I created .pdb file for dna using gabedit. But when I try to create the
topology
file I get this error: Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb
file.
Output
bject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
> Dear All,
>
> I created .pdb file for dna using gabedit. But when I try to create the
>topology file I get this error: Fatal error:
> There is a dangling bond at at least one of the terminal ends and the fo
Okay, thank you. I'll try to fix it.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
> Sorry, the pdb file is bigger than 50
l
To: Gromacs Users' List
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
> Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted
> below.
>Output of pdb2gmx is attached.
>
You have numer
Okay, I am trying AmberTools as well. Thanks Justin!
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 10, 2011 10:16:57 AM
Subject: Re: [gmx-users] Dangling bond error for dna
majid hasan wrote:
> Is there any software that g
Dear All,
I am trying to add a single strand dna, and single walled carbon nanotube in a
box using the genbox command. After typing following command:
genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o
cntdna.gro,
I get: Reading solute configuration
Containing 168
Okay, thanks Justin!.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sat, April 16, 2011 6:19:39 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
Justin A. Lemkul wrote:
>
>
> majid hasan wrote:
>> D
rs] genbox output taking forever to complete
Justin A. Lemkul wrote:
>
>
> majid hasan wrote:
>> Dear All,
>>
>> I am trying to add a single strand dna, and single walled carbon nanotube in
>> a
>>box using the genbox command. After typing following comman
er to complete
majid hasan wrote:
> Okay, so I divided the procedure in three steps, and this does produce output
>immediately. But it seems that it doesn't put second molecule inside the box.
> Here is the what I am doing:
>
> 1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 2
Okay, thank you.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 17, 2011 12:28:47 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
> Okay, so here is an output attached, for cubic box o
Alright, thanks.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 17, 2011 12:31:49 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
> Okay, so here is an output attached, for cubic box o
Dear All,
I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of
DNA around CNT in the first step, and later study the effects of temperature,
CNT length etc on the favorable geometries of hybrid.
I have created .top files for DNA, and CNT separately. To generate the top
list for GROMACS users
Sent: Sun, April 17, 2011 4:54:11 PM
Subject: Re: [gmx-users] .top file for DNA-CNT
majid hasan wrote:
> Dear All,
>
> I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of
>DNA around CNT in the first step, and later study the effect
Okay, thanks, I'll stick to Amber then.
Thanks again,
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 17, 2011 6:35:07 PM
Subject: Re: [gmx-users] .top file for DNA-CNT
majid hasan wrote:
> Okay, so I just removed #inclu
Dear All,
I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT
using Amber99, which has been used for such systems, and CNT atoms are modeled
using sp2 carbon parameters.
But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top,
and
Amber99 forcefi
ermanently down?
Thanks,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Mon, April 18, 2011 10:25:39 AM
Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield
majid hasan wrote:
> Dear All,
>
> I am doing a DNA-
Dear All,
In an attempt to create CNT topology with g_x2top and amber99, I was getting
this error: no or incorrect atomname2type.n2t file found. So I tried to create
a
atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form:
UNNAMED
400
1TUB CA1 0.392 0
, April 19, 2011 10:40:53 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
> Dear All,
>
> In an attempt to create CNT topology with g_x2top and amber99, I was getting
>this error: no or incorrect atomname2type.n2t file found. So I tried t
tin A. Lemkul
To: Discussion list for GROMACS users
Sent: Tue, April 19, 2011 10:40:53 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
> Dear All,
>
> In an attempt to create CNT topology with g_x2top and amber99, I was getting
>this error
. Lemkul
To: Gromacs Users' List
Sent: Tue, April 19, 2011 11:47:44 AM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
> Just a little addition to my previous reply: if I run the same procedure with
>oplsaa, it works. Now in Oplsaa, I added fo
Yea, sure, thanks.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Tue, April 19, 2011 12:09:06 PM
Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99
majid hasan wrote:
> Actually, I just restarted my computer, and now i
Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure
it
works) using l-bfgs integrator. When I run in the .trr output file, ends of dna
only move slightly towards cnt, but it doesn't wrap around it. Could anyone
please guide me what can be the possible issues
from mdrun on laptop?
Thanks again,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wed, April 20, 2011 11:47:09 AM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of
dna around cnt
majid hasan wrote:
&
Okay, thanks a lot.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Wed, April 20, 2011 12:01:33 PM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of
dna around cnt
majid hasan wrote:
> Okay, thanks. But t
Dear All,
I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then
ran
the mdrun with integrator = md. I am using a small ssDNA consisting of two
residues only (66 atoms), and a small CNT of about 80 atoms.
My commands are:
For energy minimization,
grompp -f lbfgs.mdp -po
AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote:
> Dear All,
>
> I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then
>ran the mdrun with integrator = md. I am using a small ssDNA consisting of two
>residues only
works better, and then I will do it
with a solvent.
Thanks,
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Thu, April 21, 2011 10:25:35 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation
majid hasan wrote:
> first .
t get distorted in md simulation
majid hasan wrote:
> Okay, so here is the file that I used for both energy minimization (with
>integrator = l-bfgs), and MD (integrator = md). Everything other than the
>value
>of integrator was same for both energy minimization and MD.
> http://phas.
Dear All,
I am doing a MD simulation of dna, and cnt in water. I get a stable simulation
in which DNA, and CNT wiggles around there positions, but they don't seem to be
attracted towards each other. CNT starts in the middle of the box and just
moves
a little, and DNA starts at top right corner
t for GROMACS users
Sent: Fri, April 22, 2011 1:51:47 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
On 4/22/2011 6:48 PM, Mark Abraham wrote:
On 4/22/2011 4:54 PM, majid hasan wrote:
>Dear All,
>>
>>
>>I am doing a MD simulation of dna,
Thanks,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Fri, April 22, 2011 10:44:45 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
> I just checked and DNA position should not be restrained be
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Fri, April 22, 2011 10:59:22 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
> Yes, ideally I didn't want to, but I read somewhere on mailing list that one
>
Okay, thanks, I'll try longer simulations.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Fri, April 22, 2011 5:18:50 PM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
majid hasan wrote:
> Okay, than
t: Re: [gmx-users] DNA not wrapping around CNT in MD simulation
On 4/23/2011 9:21 AM, majid hasan wrote:
Okay, thanks, I removed restraints from water.
>
>
> In the final simulation, I increased the simulation time from 20ps
> to
>2000ps to see if they
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