Dear gromacs users,
I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
I did next a position restraint in the
On 6/10/13 8:51 PM, Souilem Safa wrote:
Dear gromacs users,
I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o
Dear Justin,
thank you for your reply.
Yes, you are right , I have corrected it already and now it works well.
Cheers,
Safa
On 11 June 2013 09:53, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:51 PM, Souilem Safa wrote:
Dear gromacs users,
I'm trying to simulate a single molecule in
Hello,
Hi all,
I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
Hi all,
I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :
...@vt.edu
*To:* Kshatresh Dutta Dubey kshatr...@ymail.com; Discussion list for
GROMACS users gmx-users@gromacs.org
*Sent:* Tuesday, March 19, 2013 10:48 PM
*Subject:* Re: [gmx-users] Error during grompp run
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey
kshatr...@ymail.com wrote:
Dear
Dear Users
I am using groamcs 4.4.4 and when I run grompp during equilibration process, it
closes with error
Fatal error:Topology include file posre_Protein.itp not found
For more information and tips for troubleshooting, please check the GROMACS
website at
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey kshatr...@ymail.com
wrote:
Dear Users
I am using groamcs 4.4.4 and when I run grompp during equilibration
process, it closes with error
Fatal error:Topology include file posre_Protein.itp not found
For more information and tips for
On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
Fatal error:
number of coordinates in coordinate file (prot_wtr_solv.gro, 18031)
does not match topology (control.top, 16650)
It happen when i started to minimize it by using the command
grompp -v -f minim_first.mdp
to Hydrogen because the symbol
is SH?? maybe this is the source of the error and I have to redefine things in
the .n2t file?
Elie
Date: Fri, 5 Oct 2012 13:06:34 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/5/12 1:00 PM, Elie M
On 10/6/12 1:18 PM, Elie M wrote:
This is what I did. For example one of the [bonds] problems is a bond between S and one
of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S
because it si related to all-atom S: thiophenol (HS is #204); the
corresponding C
: Re: [gmx-users] Error with grompp
On 10/6/12 1:18 PM, Elie M wrote:
This is what I did. For example one of the [bonds] problems is a bond
between S and one of the carbons C in the thiophene molecule. In the n2t
file. I have added OPLSA_734 S because it si related to all-atom S
you can check
yourself in less time than it takes to send an email :)
-Justin
Elie
Date: Sat, 6 Oct 2012 13:26:38 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/6/12 1:18 PM, Elie M wrote:
This is what I did. For example one
it is a
bit weird because the bond is there in the file then why it cannot find it? Any
suggestions?
Elie
Date: Sat, 6 Oct 2012 13:59:10 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/6/12 1:57 PM, Elie M wrote:
Yes I just
On 10/6/12 2:30 PM, Elie M wrote:
Yeah sorry about that. i thought about it at the moment I was sending the
e-mail..The problem I am so desperate about getting all files correct to
minimize my polymer. It has really taken a long time. Anyhow you were right.
Switching the order did not do
they should decrease in number if things were fixed).
Am I still missing something that i should have done apart from filling in the
numbers in ffoplsaabon.itp?
Thanks
Elie
Date: Thu, 4 Oct 2012 21:25:29 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/5/12 1:00 PM, Elie M wrote:
I was able to find reasonable values of kb and b0 and inserted the info into
foplsaabon.itp. I am still getting an error; what I did is the following:
1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check
the section [atomtypes] in
[file S54.top, line 127]: No default Bond types...
Maybe the main question is for the third error is how to define these bond
types and angles?
Thank you.
Elie
Date: Wed, 3 Oct 2012 22:09:02 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 10:12 AM, Elie M wrote:
Hello everyone,
Justin, I have repeated the procedures without doing any changes and it does
seem that you were right about the broken file. However now I get a different
set of errors:
(1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of
the source of error be known and corrected?
Elie
Date: Thu, 4 Oct 2012 10:26:04 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 10:12 AM, Elie M wrote:
Hello everyone,
Justin, I have repeated the procedures without doing any
On 10/4/12 12:13 PM, Elie M wrote:
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have
commented ; one line which was given the first two errors. Now the only
errors remaining are the bonds, angles and some others. How to correct these?
For example one of
Oct 2012 12:25:48 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 12:13 PM, Elie M wrote:
Thanks a lot. I have sorted out the error that occured in the
ffoplsaabon.itp; I have commented ; one line which was given the first
On 10/4/12 4:22 PM, Elie M wrote:
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms that were not there *but present in
atomtypes.atp). The .top file
-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/4/12 4:22 PM, Elie M wrote:
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms
On 10/4/12 5:56 PM, Elie M wrote:
I guess the first parameter of each pair is easy to find. what about kb? k
theta?. kb is the force constant isnt it? any reference about a method how
to calculate them please? pr anything atht might be of help.
Bonded parameters are generally based
thinking about topologies and fixing this error.
Thank you
Elie
. Date: Tue, 2 Oct 2012 03:56:28 +
. From: emanuel.bi...@monash.edu
. Subject: RE: [gmx-users] Error with grompp
To: gmx-users@gromacs.org
Hi Elie,
Your email is a bit confusing but I will try to give you some idea
On 10/3/12 10:03 AM, Elie M wrote:
Hello Emanuel.
First of all thank you for your help. I am sorry if my previous e-mail was a
bit confusing. I will tell what I did recently.
(1) I removed all the information :molecule type, atoms, bonddihedral from my
top file and pasted them to the
@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/3/12 10:03 AM, Elie M wrote:
Hello Emanuel.
First of all thank you for your help. I am sorry if my previous e-mail was
a bit confusing. I will tell what I did recently.
(1) I removed all the information :molecule type
On 10/3/12 7:48 PM, Elie M wrote:
Sorry it seems that those breaks are due to hotmail and not present in the
topology. Thanks for your reply. I still have problems...I will tell u briefly
and as clear as possible what i did.
(1) My top file has the following lines ate first:
; Include
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found
Actually what changes I should do on the system topology, before grompp?
I found that atomtype LC3
On 10/2/12 11:26 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found
Actually what changes I should do on the system topology,
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe this error has been discussed before; I have checked previous messages on it but i
could not resolve it. I have done a modified version of the oplsaa forcefield which I
have called ffoplsaamod.n2t. The top file was created successfully.
Thanks for your time and help as always. I will see what I can do about that.
Elie
Date: Mon, 1 Oct 2012 08:38:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe this error has
to match that .top
file or what? and which file should be in the same order of which?
Thanks
Elie
Date: Mon, 1 Oct 2012 08:38:15 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Error with grompp
On 10/1/12 12:38 AM, Elie M wrote:
Dear all,
Maybe
give you some help.
Cheers,
Emanuel
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Elie M
Sent: Tuesday, 2 October 2012 1:39 PM
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Error with grompp
I am a bit confused..I am
Dear all,
Maybe this error has been discussed before; I have checked previous messages on
it but i could not resolve it. I have done a modified version of the oplsaa
forcefield which I have called ffoplsaamod.n2t. The top file was created
successfully. However when I run grompp, I get the
Hi Justin,
thank you very much for your help!!
On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work.
Hi Justin,
thank you for your answer.
Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work. Now the error is:
[ file posre_memb.itp, line 5 ]:
Atom index (4942) in position_restraints out of bounds (1-1).
This probably
On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work. Now the error is:
[ file posre_memb.itp, line 5 ]:
Hi everybody,
I want do to an energy minimization and simulation with position restraints.
Additionally to the protein I have a membrane around my protein which I
also ant to fix. If I won't fix it, it is in the whole box after the
minimization and simulation but not around my protein.
Since I
On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want do to an energy minimization and simulation with position restraints.
Additionally to the protein I have a membrane around my protein which I
also ant to fix. If I won't fix it, it is in the whole box
Hi Justin,
I wanted to use the only tip3p but I do not have the tip3p.gro file but
only the tip3p.tip file. I also have the tip4p.gro and tip5p.gro file. Can
I also use them?
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I removed all the old
On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
I wanted to use the only tip3p but I do not have the tip3p.gro file but
only the tip3p.tip file.
http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file
I also have the tip4p.gro and tip5p.gro
Okey thank you.
But shell I also
#include amber03.ff/spc.itp
Because when I don't include it I get the error:
Fatal error:
No such moleculetype SOL
An when I include it there is no error.
But in one of the last mails Justin wrote that:
You're using two different water models, so things are
On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Okey thank you.
But shell I also
#include amber03.ff/spc.itp
Because when I don't include it I get the error:
Fatal error:
No such moleculetype SOL
An when I include it there is no error.
The only thing that makes
My topology file looks like this:
4924 4940 4939 4941 4
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif
; Include water topology
#include amber03.ff/tip3p.itp
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct
On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
My topology file looks like this:
4924 4940 4939 4941 4
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif
; Include water topology
#include amber03.ff/tip3p.itp
#ifdef POSRES_WATER
;
Content of the ipt3p.itp file:
; This file is for backward compatibility only.
; Please directly include the tip3p.itp file from your force field directory.
#ifdef _FF_GROMACS
#include gmx.ff/tip3p.itp
#endif
#ifdef _FF_GROMOS96
#include gromos43a1.ff/tip3p.itp
#endif
#ifdef _FF_OPLS
#include
On 07/02/2012 07:00 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Content of the ipt3p.itp file:
; This file is for backward compatibility only.
; Please directly include the tip3p.itp file from your force field directory.
#ifdef _FF_GROMACS
#include gmx.ff/tip3p.itp
#endif
#ifdef
Ah, okey thank you. I will try to install it again.
I made the changes of the files exactly as it is descriped on the site you
wrote me. I send you in the last mail my changes in the files. Do you
think they are okey? I was not completely sure about atomtype and
residuetype and so on.
Best,
Eva
On 07/02/2012 10:07 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah, okey thank you. I will try to install it again.
I made the changes of the files exactly as it is descriped on the site you
wrote me. I send you in the last mail my changes in the files. Do you
think they are okey? I
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I have in my topology file
[ molecules ]
; Compound#mols
To: gmx-users@gromacs.org
Sent: Friday, June 29, 2012 5:24 PM
Subject: [gmx-users] error with grompp
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I
On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I
Subject: [gmx-users] error with grompp
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I have in my topology file
[ molecules
So just entering the -pname NA and -nname CL !
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Friday, June 29, 2012 5:36 PM
Subject: Re: [gmx-users] error with grompp
On 6/29/12 8
Hi Justin,
thank you for your answer.
So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA -nname CL
But when I now want to run the alraedy mentioned grompp command I get the
error:
No such
From: reising...@rostlab.informatik.tu-muenchen.de
reising...@rostlab.informatik.tu-muenchen.de
To: gmx-users@gromacs.org
Sent: Friday, June 29, 2012 5:24 PM
Subject: [gmx-users] error with grompp
Hi everybody,
I added ions to the solvent around my
On 6/29/12 9:18 AM, Shima Arasteh wrote:
So just entering the -pname NA and -nname CL !
Precisely, as genion -h instructs.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA -nname CL
This is a correct
Hi Justin,
yes I removed all the old resulting files and did everything again. So now
there is the topology and coordinate file with only NA and CL and not NA+
or CL-.
I also checked whether the molecules are listed in the same order as in
the .gro file and it is the case. So that is also
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
yes I removed all the old resulting files and did everything again. So now
there is the topology and coordinate file with only NA and CL and not NA+
or CL-.
I also checked whether the molecules are listed in
Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after packing the lipids around the
protein I always get the error the
number of
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after
Hi Justin,
thank you for your answer. Now it worked and I could do the minimization.
But now I have the same problem again but now the difference is 630.
So what I did is that I ran the minimization and everything worked. And
than I used the
perl inflategro.pl confout.gro 0.95 DPPC 0
Got it already.
Thank you!!
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I
want
to do
Hi,
I want to do a MD simulation in vacuum. So first I wanted to prepare the
files for that with grompp.
But there I got the error that
With GBSA implicit solvent, rgbradii must be equal to rlist
But the 2 values are the same in my .mdp file. Can you please show me
where the failure is?
define
On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
I want to do a MD simulation in vacuum.
So don't turn on implicit solvent.
So first I wanted to prepare the
files for that with grompp.
But there I got the error that
With GBSA implicit solvent, rgbradii must be
On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
I want to do a MD simulation in vacuum.
So don't turn on implicit solvent.
Sorry,
my fault. I want to do it in implicit solvent.
So first I wanted to prepare the
files for that with grompp.
But there I got
Hi,
After Successfully neutralizing and sd minimization of the system, I got
the below error when I try the grompp for position restrained step. The
command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
complx_eqn1.tpr
Any help will be highly appreciated.
Many thanks.
On 8/06/2012 12:23 PM, Malai wrote:
Hi,
After Successfully neutralizing and sd minimization of the system, I
got the below error when I try the grompp for position restrained
step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p
complx.top -o complx_eqn1.tpr
Any help will
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?. Can you please
guide me how to do that. Thanks.
On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/06/2012 12:23 PM, Malai wrote:
Hi,
After Successfully neutralizing and sd minimization of the
On 8/06/2012 12:34 PM, Malai wrote:
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?.
No. Using one of the two ways I suggested earlier depend what you're
actually trying to do, but since your intention in using the CA group is
unknown to us, you're preventing yourself
Dear MARK,
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?.
No. Using one of the two ways I suggested earlier depend what you're
actually trying to do, but since your intention in using the CA group is
unknown to us, you're preventing yourself getting specific help.
Hi all
I am trying to model a sulfated octasaccharide. I retrieved the
topology files from prodrg and I fixed them. The same procedure on a
the monosaccharide unit of the oligosaccharide I'm going to run worked
smoothly. After solvating the molecule, I try to pre-process it and I
obtain the
Serena Leone wrote:
Hi all
I am trying to model a sulfated octasaccharide. I retrieved the topology
files from prodrg and I fixed them. The same procedure on a the
monosaccharide unit of the oligosaccharide I'm going to run worked
smoothly. After solvating the molecule, I try to
Dear Gromacs users,
During my last simulation of 2 ns a part of a protein moved out of the water
box. When I've tried to proceed to the next 2 ns I've got the folowing message
during grompp:
Fatal error:
number of coordinates in coordinate file (wt_md2_egf4.gro, 17346)
does not match
Yulia Einav wrote:
Dear Gromacs users,
During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp:
Fatal error:
number of coordinates in coordinate file (wt_md2_egf4.gro, 17346)
Running out of box is common and it actually doesn't because of PBC. You
may just continue the simulation
For this fatal error, you shall refer to how you have created the first
tpr file: which top file you have used.
On 7/17/2007 5:39 PM, Yulia Einav wrote:
Dear Gromacs users,
During my
Furthemore the same part of the protein always move out of
the box in different simulations.
Is there any way to prevent the moving?
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Dear gmx users:
I m carrying a protein explicit solvent simulation using gromacs 3.3,
then i added water, but in next step, I m getting the following error,
grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr
:-) G R O M A C S (-:
Getting the
Dear gmx users:
I m carrying a protein explicit solvent simulation using gromacs 3.3,
then i added water, but in next step, I m getting the following error,
grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr
:-) G R O M A C S (-:
Getting the
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