[gmx-users] Re: multiple protein interaction
smriti Sebastian
smriti.sebastuan at gmail.com
Thu Jul 28 14:36:28 CEST 2011
hi,
According to the help frm gmx-users ,
I did editconf with -center option twice.concatenated the coordinate files
using cat.
Then i ran frm pdb2gmx till genbox..When I saw result pdb using pymol there
was only one protein inside the box.Why is it like that?When i opened the
gro file after pdb2gmx number of atoms were double than the original one.
wht would be the problem?please help
These are the commands which i performed:
pdb2gmx -f 1lyd.pdb -o lyzo
editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit.pdb
editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit1.pdb
cat lyzo_edit.pdb lyzo_edit1.pdb > lyzozym.pdb
pdb2gmx -f lyzozym.pdb -o lyzozy
editconf -f lyzozy -bt cubic -d 1 -center 1 -o lyzozy_edit -c
genbox -cp lyzozy_edit -cs spc216 -o lyzozy_gen.pdb
Thanks in advance
smriti
On Tue, Jul 26, 2011 at 8:09 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: multiple protein interaction (Justin A. Lemkul)
> 2. Re: OPLS for group -N=CH2 (Justin A. Lemkul)
> 3. genconf and bonded interactions (Fabio Affinito)
> 4. Re: genconf and bonded interactions (Justin A. Lemkul)
> 5. Re: genconf and bonded interactions (Fabio Affinito)
> 6. Re: genconf and bonded interactions (Justin A. Lemkul)
> 7. Re: genconf and bonded interactions (Fabio Affinito)
> 8. Re: genconf and bonded interactions (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 Jul 2011 07:39:05 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] multiple protein interaction
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2EA759.30207 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> smriti Sebastian wrote:
> > hi all,
> > I am new to GROMACS.I would like to know how we will simulate putting
> > more than two or more molecules of same proteins inside the box and do
> > simulation?Is there any possibility to replace 100 atoms or so of
> > solvent with proteins?
> > Please help.
> >
>
> You received two replies the last time you asked this exact same question:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-July/063145.html
> http://lists.gromacs.org/pipermail/gmx-users/2011-July/063146.html
>
> So what have you done to try to proceed? If you want free help, you have
> to be
> willing to use what you're given to make some progress and report back with
> specific issues that arise.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Jul 2011 07:41:22 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] OPLS for group -N=CH2
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2EA7E2.7090907 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> bhf70 at udsu.ru wrote:
> > Dear users.
> >
> > Help me.
> > What parametres of force field OPLS it is necessary to be used
> > for group -N=CH2 (imine group) ?
> >
>
> Check out the OPLS papers for suitable groups or atom types that are
> present,
> and if there's nothing already there, then you'll have to parameterize the
> group
> yourself (not a novice exercise):
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Jul 2011 15:59:14 +0200 (CEST)
> From: Fabio Affinito <f.affinito at cineca.it>
> Subject: [gmx-users] genconf and bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2EC831.7000209 at cineca.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi all,
> I used genconf because I wanted to replicate a membrane with ion channel
> on the xy plane:
> genconf -f conf.gro -o out.gro -nbox 2 2 1
>
> Then I edited by hand the .top file where I modified the number of
> molecules in the system.
>
> When attempting to run, disregarding the number of processors, the mdrun
> crashes because domain decomposition fails.
> Looking with attention to the log I find this:
> > Initializing Domain Decomposition on 4096 nodes
> > Dynamic load balancing: auto
> > Will sort the charge groups at every domain (re)decomposition
> > Initial maximum inter charge-group distances:
> > two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660
> > multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659
> > Minimum cell size due to bonded interactions: 33.959 nm
> > Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
> 1.139 nm
> > Estimated maximum distance required for P-LINCS: 1.139 nm
> > Guess for relative PME load: 0.44
> > Will use 2304 particle-particle and 1792 PME only nodes
> > This is a guess, check the performance at the end of the log file
> > Using 1792 separate PME nodes
> > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> > Optimizing the DD grid for 2304 cells with a minimum initial size of
> 42.448 nm
> > The maximum allowed number of cells is: X 1 Y 1 Z 0
>
> Now, I'm wondering why do I have such big bond interation length.. 31nm!
> I guess that the problems in the DD arises from this.
>
> Can you give me some suggestions?
>
> Thanks in advance,
>
> Fabio
>
> --
> Fabio Affinito, PhD
> SuperComputing Applications and Innovation Department
> CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
> Tel: +39 051 6171794 Fax: +39 051 6132198
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 26 Jul 2011 10:19:28 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] genconf and bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2ECCF0.6080506 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Fabio Affinito wrote:
> > Hi all,
> > I used genconf because I wanted to replicate a membrane with ion channel
> > on the xy plane:
> > genconf -f conf.gro -o out.gro -nbox 2 2 1
> >
> > Then I edited by hand the .top file where I modified the number of
> > molecules in the system.
> >
> > When attempting to run, disregarding the number of processors, the mdrun
> > crashes because domain decomposition fails.
> > Looking with attention to the log I find this:
> >> Initializing Domain Decomposition on 4096 nodes
> >> Dynamic load balancing: auto
> >> Will sort the charge groups at every domain (re)decomposition
> >> Initial maximum inter charge-group distances:
> >> two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660
> >> multi-body bonded interactions: 30.871 nm, Angle, atoms 193656
> 193659
> >> Minimum cell size due to bonded interactions: 33.959 nm
> >> Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
> >> 1.139 nm
> >> Estimated maximum distance required for P-LINCS: 1.139 nm
> >> Guess for relative PME load: 0.44
> >> Will use 2304 particle-particle and 1792 PME only nodes
> >> This is a guess, check the performance at the end of the log file
> >> Using 1792 separate PME nodes
> >> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> >> Optimizing the DD grid for 2304 cells with a minimum initial size
> >> of 42.448 nm
> >> The maximum allowed number of cells is: X 1 Y 1 Z 0
> >
> > Now, I'm wondering why do I have such big bond interation length.. 31nm!
> > I guess that the problems in the DD arises from this.
> >
> > Can you give me some suggestions?
> >
>
> Were the molecules whole in the coordinate file you replicated? If not,
> the
> bonds will now be assigned across the entire box.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 26 Jul 2011 16:28:17 +0200 (CEST)
> From: Fabio Affinito <f.affinito at cineca.it>
> Subject: Re: [gmx-users] genconf and bonded interactions
> To: gmx-users at gromacs.org
> Message-ID: <4E2ECF00.8080206 at cineca.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
>
> >
> > Were the molecules whole in the coordinate file you replicated? If not,
> > the bonds will now be assigned across the entire box.
> >
> > -Justin
> >
> Yes and not, depending on what you mean by "whole".
> It is an ion channel, so it's made of four chains.
> This clarifies? (i guess not..)
>
> F
>
> --
> Fabio Affinito, PhD
> SuperComputing Applications and Innovation Department
> CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
> Tel: +39 051 6171794 Fax: +39 051 6132198
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 26 Jul 2011 10:30:07 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] genconf and bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2ECF6F.20707 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Fabio Affinito wrote:
> > On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
> >
> >>
> >> Were the molecules whole in the coordinate file you replicated? If not,
> >> the bonds will now be assigned across the entire box.
> >>
> >> -Justin
> >>
> > Yes and not, depending on what you mean by "whole".
> > It is an ion channel, so it's made of four chains.
> > This clarifies? (i guess not..)
>
> By whole, I mean that the molecules are not split across periodic
> boundaries in
> the initial configuration that you replicated. If you replicate a periodic
> break, then you split the molecules by a distance equal to the new periodic
> distance.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 26 Jul 2011 16:35:58 +0200 (CEST)
> From: Fabio Affinito <f.affinito at cineca.it>
> Subject: Re: [gmx-users] genconf and bonded interactions
> To: gmx-users at gromacs.org
> Message-ID: <4E2ED0CE.9060009 at cineca.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
> >
> >
> > Fabio Affinito wrote:
> >> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
> >>
> >>>
> >>> Were the molecules whole in the coordinate file you replicated? If not,
> >>> the bonds will now be assigned across the entire box.
> >>>
> >>> -Justin
> >>>
> >> Yes and not, depending on what you mean by "whole".
> >> It is an ion channel, so it's made of four chains.
> >> This clarifies? (i guess not..)
> >
> > By whole, I mean that the molecules are not split across periodic
> > boundaries in the initial configuration that you replicated. If you
> > replicate a periodic break, then you split the molecules by a distance
> > equal to the new periodic distance.
> >
> > -Justin
> >
> Ok, so: no, it's not broken.
>
>
> --
> Fabio Affinito, PhD
> SuperComputing Applications and Innovation Department
> CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
> Tel: +39 051 6171794 Fax: +39 051 6132198
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 26 Jul 2011 10:38:12 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] genconf and bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E2ED154.3040502 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Fabio Affinito wrote:
> > On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
> >>
> >>
> >> Fabio Affinito wrote:
> >>> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
> >>>
> >>>>
> >>>> Were the molecules whole in the coordinate file you replicated? If
> not,
> >>>> the bonds will now be assigned across the entire box.
> >>>>
> >>>> -Justin
> >>>>
> >>> Yes and not, depending on what you mean by "whole".
> >>> It is an ion channel, so it's made of four chains.
> >>> This clarifies? (i guess not..)
> >>
> >> By whole, I mean that the molecules are not split across periodic
> >> boundaries in the initial configuration that you replicated. If you
> >> replicate a periodic break, then you split the molecules by a distance
> >> equal to the new periodic distance.
> >>
> >> -Justin
> >>
> > Ok, so: no, it's not broken.
> >
>
> What you need to do is use the information mdrun provided you to diagnose
> what's
> going on. Apparently atoms 193657 193660 are separated by 31 nm. What are
> your
> box vectors? Where are these atoms in the system? Then you'll have your
> answer. The only reason I can think of for such extreme distances is a
> periodicity issue.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> --
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>
> End of gmx-users Digest, Vol 87, Issue 138
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