[gmx-users] Running two versions of GMX at a time
chandran karunakaran
ckaru2000 at yahoo.com
Mon Sep 12 18:27:12 CEST 2011
Hi Gmx users,
Are we able to run both the lower and higher version at a time?
If possible, please help me how to do it.
with thanks
*******************************+
Dr.Karunakaran Chandran +
Biophysics Department +
Medical College of Wisconsin +
Milwaukee, WI-53226 +
Resi.: 414-443-0085 +
Off : 414-456-4034 +
********************************
--- On Tue, 30/8/11, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
Subject: gmx-users Digest, Vol 88, Issue 168
To: gmx-users at gromacs.org
Date: Tuesday, 30 August, 2011, 7:25 AM
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Today's Topics:
1. g_lie (pawan raghav)
2. Re: OPLS-AA Unknown Atomtype (Yao Yao)
3. Re: OPLS-AA Unknown Atomtype (Justin A. Lemkul)
4. MARTINI / all-atom mapping (Michael Daily)
----------------------------------------------------------------------
Message: 1
Date: Mon, 29 Aug 2011 20:49:40 +0530
From: pawan raghav <pwnrghv at gmail.com>
Subject: [gmx-users] g_lie
To: gmx-users at gromacs.org
Message-ID:
<CAD+UPv=7dRaYchD1i89T9C4QRfaNcAkYKHngkGdC=D2bCsRKtQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
g_lie calculates the deltaG= alpha(<Vl-s LJ>p - <Vl-s LJ>w) + beta(<Vl-s
el>p - <Vl-s el>w) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either <Vl-s LJ>p or <Vl-s
LJ>w and -Cqq for either <Vl-s el>p or <Vl-s el>w. My question is when
using only <Vl-s LJ>p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?
--
Pawan
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Message: 2
Date: Mon, 29 Aug 2011 12:29:39 -0700 (PDT)
From: Yao Yao <yao0o at ymail.com>
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype
To: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Message-ID:
<1314646179.30982.YahooMailNeo at web120404.mail.ne1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
HI Justin,
I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions.
So I do not think ions addition will help. And I double-checked the angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.
So I do not know any other files I may need to modify.
Thanks,
yao
________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, August 29, 2011 3:41 AM
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype
Yao Yao wrote:
> Hi Justin,
>
> Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp,
> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like,
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> Generated 338253 of the 338253 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 338253 of the 338253 1-4 parameter combinations
>
> ERROR 1 [file cro.top, line 37]:
> No default Bond types
>
>
> ERROR 2 [file cro.top, line 71]:
> No default Angle types
>
>
> ERROR 3 [file cro.top, line 72]:
> No default Angle types
>
>
> ERROR 4 [file cro.top, line 85]:
> No default Angle types
>
>
> ERROR 5 [file cro.top, line 91]:
> No default Ryckaert-Bell. types
>
>
> ERROR 6 [file cro.top, line 92]:
> No default Ryckaert-Bell. types
>
>
> ERROR 7 [file cro.top, line 93]:
> No default Ryckaert-Bell. types
>
>
> ERROR 8 [file cro.top, line 108]:
> No default Ryckaert-Bell. types
>
>
> ERROR 9 [file cro.top, line 112]:
> No default Proper Dih. types
>
>
> ERROR 10 [file cro.top, line 113]:
> No default Proper Dih. types
>
>
> ERROR 11 [file cro.top, line 114]:
> No default Proper Dih. types
>
> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file cro.top, line 142]:
> System has non-zero total charge: -1.022478e+00
>
This total charge suggests that your topology is badly broken.
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: grompp.c, line: 986
>
> Fatal error:
> There were 11 errors in input file(s)
> -----------------------------------------------
>
> I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values?
>
If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users at gromacs.org
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------------------------------
Message: 3
Date: Mon, 29 Aug 2011 15:50:45 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4E5BED95.4010803 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Yao Yao wrote:
> HI Justin,
>
> I met these errors when I grompp to do 1st-time energy minimization
> before I planned to add the ions.
> So I do not think ions addition will help. And I double-checked the
The net charge problem cannot be solved by adding ions. A fractional charge of
that magnitude indicates the charges in the topology are wrong.
> angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.
> So I do not know any other files I may need to modify.
>
The only file that contains [bondtypes], [angletypes], etc is ffoplsaabon.itp,
so if the entries are indeed there, have the correct format, and are placed
appropriately, you wouldn't be getting this error. So unless you post the exact
lines in their exact context, I'm left to assume that you've done something else
wrong.
-Justin
> Thanks,
>
> yao
>
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Monday, August 29, 2011 3:41 AM
> *Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype
>
>
>
> Yao Yao wrote:
> > Hi Justin,
> >
> > Thanks for your last reply. Now it seems that OPLS has known the
> atomtypes after I added those CA1, ... to ffoplsaanb.itp,
> > but after I claim all the angles, dihedrals, ... in the
> ffoplsaabon.itp, it still gives errors like,
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> > checking input for internal consistency...
> > processing topology...
> > Opening library file
> /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> > Opening library file
> /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> > Opening library file
> /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> > Generated 338253 of the 338253 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 338253 of the 338253 1-4 parameter combinations
> >
> > ERROR 1 [file cro.top, line 37]:
> > No default Bond types
> >
> >
> > ERROR 2 [file cro.top, line 71]:
> > No default Angle types
> >
> >
> > ERROR 3 [file cro.top, line 72]:
> > No default Angle types
> >
> >
> > ERROR 4 [file cro.top, line 85]:
> > No default Angle types
> >
> >
> > ERROR 5 [file cro.top, line 91]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 6 [file cro.top, line 92]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 7 [file cro.top, line 93]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 8 [file cro.top, line 108]:
> > No default Ryckaert-Bell. types
> >
> >
> > ERROR 9 [file cro.top, line 112]:
> > No default Proper Dih. types
> >
> >
> > ERROR 10 [file cro.top, line 113]:
> > No default Proper Dih. types
> >
> >
> > ERROR 11 [file cro.top, line 114]:
> > No default Proper Dih. types
> >
> > Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
> > Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
> > Excluding 3 bonded neighbours molecule type 'Protein'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> >
> > NOTE 1 [file cro.top, line 142]:
> > System has non-zero total charge: -1.022478e+00
> >
>
> This total charge suggests that your topology is badly broken.
>
> >
> > processing coordinates...
> > double-checking input for internal consistency...
> > renumbering atomtypes...
> > converting bonded parameters...
> >
> > There was 1 note
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0.7
> > Source code file: grompp.c, line: 986
> >
> > Fatal error:
> > There were 11 errors in input file(s)
> > -----------------------------------------------
> >
> > I do double-check those bondtypes, angles, and interactions mentioned
> in the errors, and I am pretty sure I have already declared those values
> in the ffoplsaabon.itp. Is there any other file I also need to mention
> those values?
> >
>
> If these types were actually present in ffoplsaabon.itp, then you
> wouldn't get these errors. Double check again.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Mon, 29 Aug 2011 18:55:09 -0700
From: Michael Daily <mdaily.work at gmail.com>
Subject: [gmx-users] MARTINI / all-atom mapping
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CAF-wSYEuyxzu7za2DKy1-E+xJeWb3UgC4x9TU3XTZwoi-Os_Dw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I am trying to reverse-map some martini lipids to united atom. In order to
do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I
cannot find this, only an imprecise graphic, in the MARTINI paper; the
martini.itp file doesn't appear to list which heavy atoms are represented by
each CG bead either. For example, I'm looking for something like:
'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'],
'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'],
'GL1' : ['C13', 'O14', 'C15', 'O16'],
'GL2' : ['C32', 'O33', 'C34', 'O35'],
etc.
For some atoms it's obvious which MARTINI groups they belong in, but others
on the borderline are not obvious. For example, does C12 belong in PO4 or
GL1?
Anybody have a master list like this?
Thanks,
Mike
--
====================================
Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
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