thanks in advance.
MIguel.
2010/1/26 <gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
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Today's Topics:
1. Re: the solvent group SOL is not continuous (Justin A. Lemkul)
2. Potential Energy (Yanmei Song)
3. RE?: gmx-users Digest, Vol 69, Issue 132 (ABEL Stephane 175950)
----------------------------------------------------------------------
Message: 1
Date: Tue, 26 Jan 2010 16:30:07 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] the solvent group SOL is not continuous
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b5f5edf.4080...@vt.edu <mailto:4b5f5edf.4080...@vt.edu>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Miguel Quiliano Meza wrote:
> *Hi everyone.
>
> I have a problem when I try to run GENION, GROMACS says:
> *
> WARNING: turning of free energy, will use lambda=0
> Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
> Using a coulomb cut-off of 0.9 nm
> Will try to add 0 Na ions and 15 NA+ ions.
> Select a continuous group of solvent molecules
> Opening library file /usr/share/gromacs/top/
> aminoacids.dat
> Group 0 ( System) has 275439 elements
> Group 1 ( Protein) has 1722 elements
> Group 2 ( Protein-H) has 1371 elements
> Group 3 ( C-alpha) has 185 elements
> Group 4 ( Backbone) has 555 elements
> Group 5 ( MainChain) has 741 elements
> Group 6 (MainChain+Cb) has 909 elements
> Group 7 ( MainChain+H) has 921 elements
> Group 8 ( SideChain) has 801 elements
> Group 9 ( SideChain-H) has 630 elements
> Group 10 ( Prot-Masses) has 1722 elements
> Group 11 ( Non-Protein) has 273717 elements
> Group 12 ( ZN) has 1 elements
> Group 13 ( SOL) has 273702 elements
> Group 14 ( LIG) has 14 elements
> Group 15 ( Other) has 273717 elements
> Select a group: 13
> Selected 13: 'SOL'
>
> -------------------------------------------------------
> Program genion, VERSION 3.3.3
> Source code file: ../../../../src/tools/gmx_genion.c, line: 429
>
> Fatal error:
> The solvent group SOL is not continuous: index[9]=1732,
index[10]=1747
> -------------------------------------------------------
>
> "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is."
> (Jackie Brown)
>
> *I do not know the reason,the number of residues in top file and pdb
> file are the same. The only warning that I saw was when I ran grompp:
> *
> WARNING 1 [file 1x8a.top, line unknown]:
> The largest charge group contains 11 atoms.
> Since atoms only see each other when the centers of geometry of
the charge
> groups they belong to are within the cut-off distance, too
large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a
few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2,
CO, etc.
>
> *Coincidentally they are some of the atomos of my ligand*
> *
> I have been reading the web and no-one says nothing about it. I
would be
> very grateful if someone can help me or give me advices.
>
Look at your coordinate file. Do you have two separate blocks of
solvent, like
crystal waters and then solvent added by genbox (after your zinc and
ligand,
perhaps)?
-Justin
> Best Regards
> MIguel Quiliano*
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Tue, 26 Jan 2010 14:49:40 -0700
From: Yanmei Song <yson...@asu.edu <mailto:yson...@asu.edu>>
Subject: [gmx-users] Potential Energy
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID:
<d6421a761001261349o49b01994j64acf046d9ea0...@mail.gmail.com
<mailto:d6421a761001261349o49b01994j64acf046d9ea0...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"
Dear Users:
I am in the process of setting up a new system. I have a
8.0*8.0*8.0 nm3
system which include 27800 molecules. When the system approach
equilibrium,
I found the potential energy is +3e5 (big positive number). Is this
normal?
Since based on my experience, for systems in such size, the
potential energy
is usually a big negative number? Does this mean that my force field
parameter or molecule structure have problems? Thanks in advance!
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Message: 3
Date: Tue, 26 Jan 2010 22:54:36 +0100
From: "ABEL Stephane 175950" <stephane.a...@cea.fr
<mailto:stephane.a...@cea.fr>>
Subject: [gmx-users] RE?: gmx-users Digest, Vol 69, Issue 132
To: <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID:
<f654b3ee96986e4b8dc6ef0919c88da32ab...@loderi.intra.cea.fr
<mailto:f654b3ee96986e4b8dc6ef0919c88da32ab...@loderi.intra.cea.fr>>
Content-Type: text/plain; charset="iso-8859-1"
Thanks Justin
Indeed, It worked !!!
In french, one says: "je ne dormirai pas idiot ce soir".
Stéphane
>Thank you Roland for your response
>I have effectively downloaded from the
>http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
>of gmx Unfortunately, the unpacked directory does not contain a
>configure file, I have only an configure.ac <http://configure.ac>.
>So my question is: how to obtain a fully fonctional version of 4.1
>without using git
>Thank you for your response
>
> Hi,
>
> there is currently no web-interface on the official git server. Thus
> repo.or.wz is probably the best solution.
> I checked that
http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
> up-to-date.
>
> Roland
>
> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950
<stephane.a...@cea.fr <mailto:stephane.a...@cea.fr>>wrote:
>
>
>> Hi all,
>>
>>
>>
>> For a future project, I would like to use gromacs for
simulations with the
>> CHARMM force field. I am aware that the CHARMM ff is not yet
"officially"
>> supported by gromacs, even if a paper about this port will be
published
>> soon. By reading the mailing list, I understand that a beta
version of
>> gmx4.1 is available for testing from the git depositary. I have
tried to use
>> git, but since I am behind a firewall, I cannot easily access to the
>> depositary. I have tried to obtain a previous from
>> http://repo.or.cz/w/gromacs.git through the master branch but I
am not
>> sure that the file downloaded was the latest version. Therefore,
my question
>> is how to obtain the latest version of pre gmx4.1 without using
git ?
>>
>>
>>
>> Thank you for your help
>>
>>
>>
>> Stéphane
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
>
>
>
------------------------------
Message: 3
Date: Tue, 26 Jan 2010 14:00:00 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1
without git
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b5f3bb0.1000...@vt.edu <mailto:4b5f3bb0.1000...@vt.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
Stephane Abel wrote:
> Thank you Roland for your response
>
> I have effectively downloaded from the
> http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD
version
> of gmx Unfortunately, the unpacked directory does not contain a
> configure file, I have only an configure.ac <http://configure.ac>.
>
> So my question is: how to obtain a fully fonctional version of 4.1
> without using git
>
In the code you downloaded, there should be a script called
"bootstrap" which
you can execute to generate the configure file.
-Justin
> Thank you for your response
>>
>> Hi,
>>
>> there is currently no web-interface on the official git server. Thus
>> repo.or.wz is probably the best solution.
>> I checked that
http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
>> up-to-date.
>>
>> Roland
>>
>> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950
>> <stephane.a...@cea.fr <mailto:stephane.a...@cea.fr>>wrote:
>>
>>
>>> Hi all,
>>>
>>>
>>>
>>> For a future project, I would like to use gromacs for simulations
>>> with the
>>> CHARMM force field. I am aware that the CHARMM ff is not yet
>>> "officially"
>>> supported by gromacs, even if a paper about this port will be
published
>>> soon. By reading the mailing list, I understand that a beta
version of
>>> gmx4.1 is available for testing from the git depositary. I have
tried
>>> to use
>>> git, but since I am behind a firewall, I cannot easily access
to the
>>> depositary. I have tried to obtain a previous from
>>> http://repo.or.cz/w/gromacs.git through the master branch but I
am not
>>> sure that the file downloaded was the latest version. Therefore, my
>>> question
>>> is how to obtain the latest version of pre gmx4.1 without using
git ?
>>>
>>>
>>>
>>> Thank you for your help
>>>
>>>
>>>
>>> Stéphane
>>>
>>> --
>>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>
>>
>>
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Wed, 27 Jan 2010 08:09:47 +1100
From: "Dallas B. Warren" <dallas.war...@pharm.monash.edu.au
<mailto:dallas.war...@pharm.monash.edu.au>>
Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme
tutorial
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID:
<89907ea1dcfb7548a431c13a270f9dd508fd8...@prk-exch-01.vcp.local>
Content-Type: text/plain; charset="us-ascii"
So, what EXACTLY are you doing?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
<mailto:dallas.war...@pharm.monash.edu.au>
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
From: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] On Behalf Of vivek sharma
Sent: Monday, 25 January 2010 7:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme
tutorial
HI Tsjerk,
Thanks for your reply. But, I can't see if it is going suddenly or
gradually.
What i can see is the ligand is away from the molecule after editing the
gro file with PRODRG output.
It seems liek PRODRG has modified the co-ordinates that places ligand
away from the protein.
~Vivek
2010/1/25 Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>>
Hi Vivek,
> Now when I am processing the modified .gro file to generate box, the
ligand
> and cofactor are going away from the protein molecule and I am not
able to
> analyze the complex.
Gradually going away, or suddenly jumping?
In the latter case, read up on periodic boundary conditions.
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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Message: 5
Date: Tue, 26 Jan 2010 16:26:09 -0500
From: Miguel Quiliano Meza <rifaxim...@gmail.com
<mailto:rifaxim...@gmail.com>>
Subject: [gmx-users] the solvent group SOL is not continuous
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<6c2f55e31001261326w7d3a2588wf577aa5b3f661...@mail.gmail.com
<mailto:6c2f55e31001261326w7d3a2588wf577aa5b3f661...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of solvent molecules
Opening library file /usr/share/gromacs/top/
aminoacids.dat
Group 0 ( System) has 275439 elements
Group 1 ( Protein) has 1722 elements
Group 2 ( Protein-H) has 1371 elements
Group 3 ( C-alpha) has 185 elements
Group 4 ( Backbone) has 555 elements
Group 5 ( MainChain) has 741 elements
Group 6 (MainChain+Cb) has 909 elements
Group 7 ( MainChain+H) has 921 elements
Group 8 ( SideChain) has 801 elements
Group 9 ( SideChain-H) has 630 elements
Group 10 ( Prot-Masses) has 1722 elements
Group 11 ( Non-Protein) has 273717 elements
Group 12 ( ZN) has 1 elements
Group 13 ( SOL) has 273702 elements
Group 14 ( LIG) has 14 elements
Group 15 ( Other) has 273717 elements
Select a group: 13
Selected 13: 'SOL'
-------------------------------------------------------
Program genion, VERSION 3.3.3
Source code file: ../../../../src/tools/gmx_genion.c, line: 429
Fatal error:
The solvent group SOL is not continuous: index[9]=1732, index[10]=1747
-------------------------------------------------------
"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is."
(Jackie
Brown)
*I do not know the reason,the number of residues in top file and pdb
file
are the same. The only warning that I saw was when I ran grompp:
*
WARNING 1 [file 1x8a.top, line unknown]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the
charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few
atoms.
For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.
*Coincidentally they are some of the atomos of my ligand*
*
I have been reading the web and no-one says nothing about it. I would be
very grateful if someone can help me or give me advices.
Best Regards
MIguel Quiliano*
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