[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 118
Prasanna Dr
adveirprasanna at gmail.com
Tue Mar 29 07:25:04 CEST 2016
Hi,
Thanks for your quick response.
AMBER mmpbsa does amino-acid pairwise residue decomposition. Pairwise
decomposition energy is very suitable input for weighted network analysis
(to understand the information flow between residues and to find key
amino-acids of a functional protein). I tried to convert gromacs parameters
into AMBER parameters, but I couldn't get success as I am using modified
force field in gromacs. So values of pairwise residue decomposition is
important for further analysis (Reference:
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b00946). I want do similar
kind of analysis as of reference article using g_mmpbsa (rashmikumari and
group) of gromacs.
Hi,
Probably you can find a way to compute a number with this non-GROMACS tool.
But is there any evidence to support that such a number will mean anything?
MM force fields are pairwise additive, not decomposable.
Mark
On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:
> Hi
>
> I have been using g_mmpbsa of Rashhmi Kumari and group to calculate
binding
> energy of lipids in protein-lipid complex. I got a quite good results with
> g_mmpbsa. Now, In my next step I need to perform network analysis where
> pairwise interaction energy from mmpbsa will be considered.
>
> I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> generated residue decomposition energy of aminoacids with lipid (not
> between aminoacids) as shown below (for example purpose)
>
> 1 1.0784
> 2 -0.0261
> 3 0.9493
> 4 0.0206
> 5 -0.0583
> 6 0.0061
> 7 -0.0278
> .
> .
> .
> 450
>
> While running mmpbsa my first input was protein and second input was lipid
> (in place of ligand). Now I have interaction energy of each aminoacid with
> lipid .
>
> Now, I need interaction energy between aminoacids. like 1st aminoacid
with
> remaining 499 aminoacid and 2nd with remaining 449 aminoacids and so on.
>
> Is it possible to calculate interaction energy between amnoacids and with
> lipids using g_mmpbsa (n X n matrix of energy values) ?
>
> --
> D R Prasanna
On Mon, Mar 28, 2016 at 9:11 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Query on g_mmpbsa in gromacs (Prasanna Dr)
> 2. Re: Running Gromacs on clusters (Ray Chao)
> 3. Postdoctoral opening in biomolecular modeling at IBM (Payel Das)
> 4. Re: Running Gromacs on clusters (Mark Abraham)
> 5. Re: Query on g_mmpbsa in gromacs (Mark Abraham)
> 6. Re: Query on g_mmpbsa in gromacs (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 Mar 2016 18:07:18 +0530
> From: Prasanna Dr <adveirprasanna at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Query on g_mmpbsa in gromacs
> Message-ID:
> <CANJ1hSOYRcKL+dcioLM_w5HMY_kegz9Yr-3A=
> aE8rGyXvB98-Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi
>
> I have been using g_mmpbsa of Rashhmi Kumari and group to calculate binding
> energy of lipids in protein-lipid complex. I got a quite good results with
> g_mmpbsa. Now, In my next step I need to perform network analysis where
> pairwise interaction energy from mmpbsa will be considered.
>
> I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> generated residue decomposition energy of aminoacids with lipid (not
> between aminoacids) as shown below (for example purpose)
>
> 1 1.0784
> 2 -0.0261
> 3 0.9493
> 4 0.0206
> 5 -0.0583
> 6 0.0061
> 7 -0.0278
> .
> .
> .
> 450
>
> While running mmpbsa my first input was protein and second input was lipid
> (in place of ligand). Now I have interaction energy of each aminoacid with
> lipid .
>
> Now, I need interaction energy between aminoacids. like 1st aminoacid with
> remaining 499 aminoacid and 2nd with remaining 499 aminoacids and so on.
>
> Is it possible to calculate interaction energy between amnoacids and with
> lipids using g_mmpbsa (n X n matrix of energy values) ?
>
> --
> D R Prasanna
> Research Scholar
> Computational Biophysics Group
> Department of Biotechnology
> Indian Institute of Technology Madras
> Chennai
> Tamilnadu-600036
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 28 Mar 2016 10:39:00 -0400
> From: Ray Chao <xiaoainisa at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Running Gromacs on clusters
> Message-ID:
> <
> CAFm40rDcp4pVazRivetRg2pi9JnBBQd5CRu_g0OBdXJnsdYuLA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> H
> ?i, Mark,
>
> Does that mean the Gromacs on our cluster is not compiled as MPI-enabled?
>
> Thanks.?
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 28 Mar 2016 09:51:36 -0500
> From: "Payel Das" <daspa at us.ibm.com>
> To: "Discussion list for GROMACS users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Postdoctoral opening in biomolecular modeling at
> IBM
> Message-ID: <201603281451.u2SEpcJv006413 at d01av03.pok.ibm.com>
> Content-Type: text/plain; charset="US-ASCII"
>
> Postdoctoral position available at IBM T J Watson Research Center. For
> details please see
>
> https://krb-sjobs.brassring.com/TGWebHost/jobdetails.aspx?partnerid=26059&siteid=5016&AReq=34229BR
> . If interested, please contact daspa at us.ibm.com.
>
> ------
> Payel Das, Ph.D.
> Research Staff Scientist
> Neuroeducation Lead, Learning Sciences and Cognitive Computing Department
> IBM Thomas J. Watson Research Center
> Yorktown Heights, NY 10598
> Ph:914-945-2373
> Webpage: https://researcher.ibm.com/researcher/view.php?person=us-daspa
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 28 Mar 2016 15:38:52 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Running Gromacs on clusters
> Message-ID:
> <
> CAMNuMAR3_vOqkS5S6cx2Vr5TGZgnQhRY2NqNsJ4CMHtTCdX9hg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Maybe. I can't tell, because that's just a default, not a fixed behaviour.
> But you can run gmx -version to find things out, and talk to whoever
> installed it.
>
> Mark
>
> On Mon, 28 Mar 2016 16:39 Ray Chao <xiaoainisa at gmail.com> wrote:
>
> > H
> > ?i, Mark,
> >
> > Does that mean the Gromacs on our cluster is not compiled as MPI-enabled?
> >
> > Thanks.?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 28 Mar 2016 15:41:10 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Query on g_mmpbsa in gromacs
> Message-ID:
> <CAMNuMARrzuC=
> habbF+U3wj4f+3SjBYU1HFX+CED-SMg_w0ncnw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Probably you can find a way to compute a number with this non-GROMACS tool.
> But is there any evidence to support that such a number will mean anything?
> MM force fields are pairwise additive, not decomposable.
>
> Mark
>
> On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:
>
> > Hi
> >
> > I have been using g_mmpbsa of Rashhmi Kumari and group to calculate
> binding
> > energy of lipids in protein-lipid complex. I got a quite good results
> with
> > g_mmpbsa. Now, In my next step I need to perform network analysis where
> > pairwise interaction energy from mmpbsa will be considered.
> >
> > I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> > generated residue decomposition energy of aminoacids with lipid (not
> > between aminoacids) as shown below (for example purpose)
> >
> > 1 1.0784
> > 2 -0.0261
> > 3 0.9493
> > 4 0.0206
> > 5 -0.0583
> > 6 0.0061
> > 7 -0.0278
> > .
> > .
> > .
> > 450
> >
> > While running mmpbsa my first input was protein and second input was
> lipid
> > (in place of ligand). Now I have interaction energy of each aminoacid
> with
> > lipid .
> >
> > Now, I need interaction energy between aminoacids. like 1st aminoacid
> with
> > remaining 499 aminoacid and 2nd with remaining 499 aminoacids and so on.
> >
> > Is it possible to calculate interaction energy between amnoacids and with
> > lipids using g_mmpbsa (n X n matrix of energy values) ?
> >
> > --
> > D R Prasanna
> > Research Scholar
> > Computational Biophysics Group
> > Department of Biotechnology
> > Indian Institute of Technology Madras
> > Chennai
> > Tamilnadu-600036
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 28 Mar 2016 15:41:10 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Query on g_mmpbsa in gromacs
> Message-ID:
> <CAMNuMARrzuC=
> habbF+U3wj4f+3SjBYU1HFX+CED-SMg_w0ncnw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Probably you can find a way to compute a number with this non-GROMACS tool.
> But is there any evidence to support that such a number will mean anything?
> MM force fields are pairwise additive, not decomposable.
>
> Mark
>
> On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:
>
> > Hi
> >
> > I have been using g_mmpbsa of Rashhmi Kumari and group to calculate
> binding
> > energy of lipids in protein-lipid complex. I got a quite good results
> with
> > g_mmpbsa. Now, In my next step I need to perform network analysis where
> > pairwise interaction energy from mmpbsa will be considered.
> >
> > I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> > generated residue decomposition energy of aminoacids with lipid (not
> > between aminoacids) as shown below (for example purpose)
> >
> > 1 1.0784
> > 2 -0.0261
> > 3 0.9493
> > 4 0.0206
> > 5 -0.0583
> > 6 0.0061
> > 7 -0.0278
> > .
> > .
> > .
> > 450
> >
> > While running mmpbsa my first input was protein and second input was
> lipid
> > (in place of ligand). Now I have interaction energy of each aminoacid
> with
> > lipid .
> >
> > Now, I need interaction energy between aminoacids. like 1st aminoacid
> with
> > remaining 499 aminoacid and 2nd with remaining 499 aminoacids and so on.
> >
> > Is it possible to calculate interaction energy between amnoacids and with
> > lipids using g_mmpbsa (n X n matrix of energy values) ?
> >
> > --
> > D R Prasanna
> > Research Scholar
> > Computational Biophysics Group
> > Department of Biotechnology
> > Indian Institute of Technology Madras
> > Chennai
> > Tamilnadu-600036
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 143, Issue 118
> *******************************************************
>
--
D R Prasanna
Research Scholar
Computational Biophysics Group
Department of Biotechnology
Indian Institute of Technology Madras
Chennai
Tamilnadu-600036
Ph: 09962026963
More information about the gromacs.org_gmx-users
mailing list