Dear Yanmei Song：
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When
I run pdb2gmx using my molecules with the command:
pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3
I got the error message:
Opening library file ffG45a3.rtp
Opening
Dear Yanmei Song：
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When
I run pdb2gmx using my molecules with the command:
pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3
I got the error message:
Opening library file ffG45a3.rtp
Opening library file
- Original Message -
From: 佘安奇 she_an...@yahoo.cn
Date: Wednesday, May 19, 2010 16:17
Subject: [gmx-users] [gmx-user]Error by pdb2gmx
To: gmx-users@gromacs.org
---
| Dear Yanmei Song：
I used gromacs version 3.3.1. I update
Thanks mark, but I think that g_anaeig calculates the degree of overlap then
what method would you use to calculate this?
--
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- Original Message -
From: pawan raghav pwnr...@gmail.com
Date: Wednesday, May 19, 2010 16:28
Subject: [gmx-users] RMSIP
To: gmx-users@gromacs.org
Thanks mark, but I think that g_anaeig calculates the degree of overlap then
what method would you use to calculate this?
I don't know
Hi Justin,
Thank you for your help, But when I run x2top command there is one error that
is:Can not find forcefield for atom C1-1 with 2 bondsCan not find forcefield
for atom C4-4 with 2 bonds...Program x2top, VERSION 4.0.5Source code file:
x2top.c, line: 207Fatal error:Could only find a
but genion only accepts one type of ion, how can we insert different types?
On Tue, May 18, 2010 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu wrote:
tahereh tekieh wrote:
dear friends
i want to simulate a water medium in which 5 types of different ions flow
in it. how can i do that with
- Original Message -
From: tahereh tekieh golesan...@gmail.com
Date: Wednesday, May 19, 2010 17:09
Subject: Re: [gmx-users] water medium
To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org
but genion only accepts one type of ion, how can we insert different
Hi,
there was a problem in do_dssp when used on proteins with more
than 10 chains. Is this the case? I just saw that I
only fixed that in the head, but not in 4.0.x.
Carsten
On May 18, 2010, at 3:49 PM, shahid nayeem wrote:
Hi
When I run dssp alone with a .pdb file it works well. But
Hi,
The answer is given by g_anaeig (-h):
When -v, -eig, -v2 and -eig2 are given, a single number for the overlap
between the covariance matrices is generated. The formulas are:
difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))
normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
:
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Hi,
I want to calculate the solvation free energy of Wild-type human IAPP
(hIAPP) with 37 residues in length that residu26 isoleucine is mutated to
proline (ile26pro). I used dual topology in Thermodynamic integration (TI)
for calculating salvation free energy. For the solvation free energy
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you zou wrote:
Hi Justin,
Thank you for your help, But when I run x2top command there is one error
that is:
Can not find forcefield for atom C1-1 with 2 bonds
Can not find forcefield for atom C4-4 with 2 bonds
...
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal
Hello All
This question may sound trivial to many, but as i am new to this field, please
help.
I want to ask a question regarding my previous query of distortion of protein
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent
Can you not run pdb2gmx for each of your molecules that you want separate
force fields for? Then cat the gro files, renumber and include the molecule
types as .itp files in the .top file as below. If I'm doing anything wrong
please let me know! :)
;
;This is your topology file
;What If
sonali dhindwal wrote:
Hello All
This question may sound trivial to many, but as i am new to this field,
please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
Can you provide a link to your previous post,
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using
Oliver Grant wrote:
Can you not run pdb2gmx for each of your molecules that you want
separate force fields for? Then cat the gro files, renumber and include
the molecule types as .itp files in the .top file as below. If I'm doing
anything wrong please let me know! :)
Combining different
Hello All
This question may sound trivial to many, but as i am new to this field, please
help.
I want to ask a question regarding my previous query of distortion of protein
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using
Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.
I am pasting .mdp file which I used for MD simulation :
title = trp_drg MD
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt
sonali dhindwal wrote:
Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.
Then you should do energy minimization after constructing the system.
I am pasting .mdp file which I used for MD simulation :
title = trp_drg MD
cpp
Sorry, but I couldnt get your question,
I have used this .mdp file for energy minimisation after addition of water and
using GROMOS96 43a1 force field :
title = drg_trp
cpp = /lib/cpp ; location of cpp on SGI
define = -DFLEX_SPC ; Use Ferguson’s Flexible water
After adding water you can do energy minimization (EM) in two steps:
1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.
The above three steps will help hydrate the protein molecule with minimal
Gaurav Goel wrote:
After adding water you can do energy minimization (EM) in two steps:
1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the protein backbone.
The above three steps will help hydrate the protein molecule
Dear All
I’m trying to obtain RMSD distribution of a ligand in the binding site of the
receptor protein during 40 ns MD simulation.
Could you please explain:
- what is exactly the yaxis unit of the plot obtained using g_cluster with
–dist option
- how is this distribution calculated?
Thank
On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Gaurav Goel wrote:
After adding water you can do energy minimization (EM) in two steps:
1. Constrain the protein backbone and do EM.
2. Now do EM on the full system.
3. Run a short MD simulation by constraining the
Hi,
I wanna keep crystallographic water with tip4p model for md simulation
but when I use pdb2gmx even if I set -water tip4p it protonates oxygens to
spc water model instead.
Is there any way to replace spc water molecules with tip4p water
molecules in the same orientation?
What's your GROMACS
Thanks Justin for your help
I checked the mdout.mpd, all the parameters were interpereted correctly, though
from next time i will take care of putting space.
regarding you asked if those are small molecules, yes those are the ligands and
i have taken .itp and .gro file from Dundee Prodrg server.
sonali dhindwal wrote:
Thanks Justin for your help
I checked the mdout.mpd, all the parameters were interpereted correctly,
though from next time i will take care of putting space.
regarding you asked if those are small molecules, yes those are the
ligands and i have taken .itp and .gro file
how can it be fixed?
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Date: Wed, 19 May 2010 19:31:30 +0530 (IST)
From
Hi,
The distribution is calculated as follows:
101 bins are formed between zero and maximum rmsd in equal separation
(by calculating the largest value by 100 to create the separation). Each
rmsd value is put into the right bin and the counter for that bin is
increased by 1. The total number of
Hi again, Sorry I confused you with my question. My question is How can I make
.gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I
can use x2top command I will make .top file just, is it true? I think .gro file
is dependent on forcefiled too so If I use editconf
Dear all,
When I try to simulation with NVE ensemble, the
total energy keeps decreasing. Geometry optimization
and solvent equilibration are done before the NVE simulation.
I follow the requirements provided in
http://www.gromacs.org/Documentation/Terminology/NVE
Would any one help me to
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on this website
http://www.pharmacy.manchester.ac.uk/bryce/amber#box
i found a gorgeous little box containing a pretty number of 6-site
modeled AN molecules,
Hi,
You could use acpype, although you will need to push more than one button :-)
http://code.google.com/p/acpype/
Cheers,
Rui Rodrigues
On Wed, 19 May 2010 18:15:29 +0200, vedat durmaz wrote
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent
you zou wrote:
Hi again,
Sorry I confused you with my question. My question is How can I make .gro
file and .top file from drug.pdb (that removed from drug-enzyme.pdb)?
If I can use x2top command I will make .top file just, is it true? I think
.gro file is dependent on forcefiled too so If I
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on this website
http://www.pharmacy.manchester.ac.uk/bryce/amber#box
i found a gorgeous little box containing a pretty number of 6-site
modeled AN
Hi,
I am trying to look at the free energy differences as a function of
end-to-end distance of peptides in water. I am running a set of simulations
with the two atoms of interest joined by a type 2 constraint, with the length
varying from 0.5 to 3 nm. However, these simulations all
I did it for other solvent. If you have AMBER is very easy to do. Do
you have AMBER?
On Wed, May 19, 2010 at 12:15 PM, vedat durmaz dur...@zib.de wrote:
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on
thanks to all so far
@anthony
i have amberTools, but not the amber MD package. is that enough for my
purpose?
@rui
acpypi -i ch3cn_210.pdb
says: cannot find template for residue C3N in our library. and indeed,
there's no residue C3N in my ffamber99sb.rtp file
(and i don't know, how to use it
Hi,
I have two questions concerning generating a solvent box for my protein using
gromacs 3.3.1.
1) I used to use editconf to generate a dodecahedron box, then use genbox. It
used to work fine:
$editconf -f protein.gro -o protein_box.gro -d 0.9 -bt dodecahedron -c
$genbox -cp protein_box.gro
Lin Xu wrote:
Hi, I have two questions concerning generating a solvent box for my protein
using gromacs 3.3.1.
Any particular reason you're using software that is over four years old?
Gromacs 4.0.7 will give you a major speed upgrade, and lots of new features.
1) I used to use editconf
Hi All,
I understand that the error of segmentation fault may come from many
reasons, but I just couldn't figure out the reason of this error in my
simulations. I want to run md simulations with explicit water for 20
structures of one domain (residue 77-148) of calmodulin (PDB 1CFC).
For more exotic NVE-systems I had to do some or several of the following
things to get stable Etot:
* have an even shorter timestep than one would expect from the applied
constraints and such.
* use double precision.
* apply the constraints with lower tolerance/more iterations etc.
Then
Lan Hua wrote:
Hi All,
I understand that the error of segmentation fault may come from
many reasons, but I just couldn't figure out the reason of this error in
my simulations. I want to run md simulations with explicit water for 20
structures of one domain (residue 77-148) of
Dear Vedat,
On Wed, May 19, 2010 at 20:36, gmx-users-requ...@gromacs.org wrote:
@rui
acpypi -i ch3cn_210.pdb
says: cannot find template for residue C3N in our library. and indeed,
there's no residue C3N in my ffamber99sb.rtp file
(and i don't know, how to use it in order to generate my
Hello,
I am trying to get only interaction energies (vdw and electrostatics)
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in
the system. I have added *exclusions section* at the end of top file to
exclude all nonbonded interactions between atom 1 and all other 20 atoms.
Hi Justin,
Thank you so much for your quick reply and good suggestions. The
following is my answer.
On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Lan Hua wrote:
Hi All,
I understand that the error of segmentation fault may come from many
reasons, but
Moeed wrote:
Hello,
I am trying to get only interaction energies (vdw and electrostatics)
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules
in the system. I have added _exclusions section_ at the end of top file
to exclude all nonbonded interactions between atom 1 and
Lan Hua wrote:
Hi Justin,
Thank you so much for your quick reply and good suggestions. The
following is my answer.
On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Lan Hua wrote:
Hi All,
I understand that
I seem to say this several times per week: in my experience (and in
the
experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG page on the
GROMACS website
Dallas B. Warren wrote:
I seem to say this several times per week: in my experience (and in
the
experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG
Hi Justin,
I appreciated your quick answers. So if I understand correctly, using
constraints = hbonds with the time step of 2fs, it should be fine, right?
Thanks,
Lan
On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Lan Hua wrote:
Hi Justin,
Thank you so
Lan Hua wrote:
Hi Justin,
I appreciated your quick answers. So if I understand correctly,
using constraints = hbonds with the time step of 2fs, it should be fine,
right?
Maybe. If your goal is REMD (I'm not clear from your original post) then
stability may be an issue at higher
Thanks. The simulations are regular MD in explicit water at room
temperature.
Lan
On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Lan Hua wrote:
Hi Justin,
I appreciated your quick answers. So if I understand correctly, using
constraints = hbonds with the
Dear Mark:
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. And
the rtp of my molecule is in the attached file DRG.txt.
Thank you very much!
Angel
[ DRG2 ]
[ atoms ]
CCN CH3 0.0 1
CCM CH1 0.08300 2
CCO CH3 0.03300 2
Hello Justin,
Thanks for your comments. Actually, since I am interested in only
interaction energies *between* molecules I thought by excluding energies
between atoms on a single chain what I get from nonbonded interactions would
not include 1-4 interactions.
Hello,
I have a system of dimers which spontaneously assemble into clusters.
I would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of clusters
vs time, the average cluster size vs time and a histogram of the
On 2010-05-20 04.55, toma0...@umn.edu wrote:
Hello,
I have a system of dimers which spontaneously assemble into clusters. I
would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of
clusters vs time, the average cluster
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