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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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" <jalem...@vt.edu> > Subject: Re: [gmx-users] multiple protein interaction > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2ea759.30...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] OPLS for group -N=CH2 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2ea7e2.7090...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > bh...@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.affin...@cineca.it> > Subject: [gmx-users] genconf and bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2ec831.7000...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] genconf and bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2eccf0.6080...@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.affin...@cineca.it> > Subject: Re: [gmx-users] genconf and bonded interactions > To: gmx-users@gromacs.org > Message-ID: <4e2ecf00.8080...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] genconf and bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2ecf6f.20...@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.affin...@cineca.it> > Subject: Re: [gmx-users] genconf and bonded interactions > To: gmx-users@gromacs.org > Message-ID: <4e2ed0ce.9060...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] genconf and bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e2ed154.3040...@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 > > ======================================== > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@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! > > End of gmx-users Digest, Vol 87, Issue 138 > ****************************************** >
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