Hi , Justin. well.. I keep three water molecules from original PDB , my actual model was obtained by homology.
my file *top shows this. [ molecules ] ; Compound #mols Protein 1 ----------> Also, Zn+2 is here SOL 3 --------> from template LIG 1 SOL 91231------->added with genbox Now, in my *pdb file obtained with genbox there are no blocks, ............... ........................... ATOM 1721 O1 SER 185 78.315 86.779 66.412 1.00 0.00 ATOM 1722 O2 SER 185 78.467 89.180 66.704 1.00 0.00 ATOM 1723 Zn ZN 186 70.487 59.483 68.899 1.00 0.00 ATOM 1724 OW HOH 187 69.331 58.199 67.904 1.00 0.00 ATOM 1725 HW1 HOH 187 70.147 58.199 68.481 1.00 0.00 ATOM 1726 HW2 HOH 187 68.515 58.199 68.481 1.00 0.00 ATOM 1727 OW HOH 188 70.810 60.669 67.316 1.00 0.00 ATOM 1728 HW1 HOH 188 71.626 60.669 67.893 1.00 0.00 ATOM 1729 HW2 HOH 188 70.810 61.485 66.739 1.00 0.00 ATOM 1730 OW HOH 189 68.765 60.471 69.225 1.00 0.00 ATOM 1731 HW1 HOH 189 69.581 60.471 69.802 1.00 0.00 ATOM 1732 HW2 HOH 189 68.765 59.655 68.648 1.00 0.00 ATOM 1733 CAB LIG 190 71.884 63.353 62.792 1.00 0.00 ATOM 1734 HAB LIG 190 70.812 63.372 62.596 1.00 0.00 ........................................ ...................... ........ ATOM 1746 HAI LIG 190 72.792 64.517 66.353 1.00 0.00 ATOM 1747 OW SOL 191 5.690 12.751 11.651 1.00 0.00 ATOM 1748 HW1 SOL 191 4.760 12.681 11.281 1.00 0.00 ATOM 1749 HW2 SOL 191 5.800 13.641 12.091 1.00 0.00 ATOM 1750 OW SOL 192 15.551 15.111 7.030 1.00 0.00 ATOM 1751 HW1 SOL 192 14.981 14.951 7.840 1.00 0.00 ..... .............. What could be the problem?? thanks in advance. MIguel. 2010/1/26 <gmx-users-requ...@gromacs.org> > 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: 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> > Subject: Re: [gmx-users] the solvent group SOL is not continuous > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <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 | (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> > Subject: [gmx-users] Potential Energy > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100126/e10b926a/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 26 Jan 2010 22:54:36 +0100 > From: "ABEL Stephane 175950" <stephane.a...@cea.fr> > Subject: [gmx-users] RE?: gmx-users Digest, Vol 69, Issue 132 > To: <gmx-users@gromacs.org> > Message-ID: > <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. > > >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 > >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 > >> 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. > >> 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> > 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> > Message-ID: <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. > > > > 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>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 > >>> 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. > >>> 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 | (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> > Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme > tutorial > To: Discussion list for GROMACS users <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 > +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] 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> > > 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 > -- > > 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/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. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100127/41f072dc/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Tue, 26 Jan 2010 16:26:09 -0500 > From: Miguel Quiliano Meza <rifaxim...@gmail.com> > Subject: [gmx-users] the solvent group SOL is not continuous > To: gmx-users@gromacs.org > Message-ID: > <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* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100126/8081ed19/attachment.html > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 69, Issue 132 > ****************************************** > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/ms-tnef > Size: 7377 bytes > Desc: not available > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100126/599c6036/attachment.bin > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 69, Issue 133 > ****************************************** >
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