Re: [gmx-users] ramachandran plot
> Message: 4 > Date: Wed, 9 Jan 2019 11:59:31 +0100 > From: Tamas Hegedus > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] ramachandran plot > Message-ID: <563a0c65-532e-a47d-fdf7-5046a062c...@hegelab.org> > Content-Type: text/plain; charset=utf-8; format=flowed Hi Tamas Thank you so much for your suggestion. I will check that. Just to know one more thing, is there any program to know only number of residues in the allowed and favoured region in the output? Thank You > Hi, > > I use the python MDAnalysis packages for this. > > https://github.com/MDAnalysis/mdanalysis/issues/1335 > > https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html > > Have a nice day, Tamas > > On 01/09/2019 10:30 AM, za...@tezu.ernet.in wrote: >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> India >> >> >> >> >> >> >> >> * * * D I S C L A I M E R * * * >> This e-mail may contain privileged information and is intended solely >> for the individual named. If you are not the named addressee you should >> not disseminate, distribute or copy this e-mail. Please notify the >> sender immediately by e-mail if you have received this e-mail in error >> and destroy it from your system. Though considerable effort has been >> made to deliver error free e-mail messages but it can not be guaranteed >> to be secure or error-free as information could be intercepted, >> corrupted, lost, destroyed, delayed, or may contain viruses. The >> recipient must verify the integrity of this e-mail message. >> > > > -- > Tamas Hegedus, PhD > Senior Research Fellow > Department of Biophysics and Radiation Biology > Semmelweis University | phone: (36) 1-459 1500/60233 > Tuzolto utca 37-47| mailto:ta...@hegelab.org > Budapest, 1094, Hungary | http://www.hegelab.org > > > -- Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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-requ...@gromacs.org.
Re: [gmx-users] ramachandran plot
> Message: 5 > Date: Wed, 9 Jan 2019 17:17:31 +0530 > From: Subhomoi Borkotoky > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ramachandran plot > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Hii Subhomoi Thank you so much for your suggestion. Regards Zaved > Hi Javed, > > I hope *gmx rama* will solve the issue. > > http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html > > > Thanks & Regards, > -- > *Subhomoi Borkotoky, Ph. D.* > DBT Research Associate, > Kusuma School of Biological Sciences, > Indian Institute of Technology Delhi, > New Delhi-110016, > India. > > Alternate E-mail : subho...@yahoo.com > > > > > > On Wed, Jan 9, 2019 at 3:01 PM wrote: > >> Dear Users >> >> Can anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >> India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
Hi, Yes the value given to pdb2gmx -water is not configurable in this way. I suggest you use normal tip4p and edit the resulting topol.top file to specify the include file you really need. Mark On Fri., 11 Jan. 2019, 02:55 Justin Lemkul, wrote: > > > On 1/10/19 11:51 AM, ZHANG Cheng wrote: > > I think using "-water tip4pd" will always cause errors, without allowing > me to select the forcefield. I also put the ff directory to my launching > folder, but still the same problem. > > > > > > Simply using "-water tip4p" will allow me to select the forcefield. But > I want to use tip4pd, not tip4p. > > > > Turns out you'll have to make the selection interactively or otherwise > change the pdb2gmx source code to allow for a new water model to be > selected. > > -Justin > > > > > > > The below is the error message. > > > > > > GROMACS: gmx pdb2gmx, version 2018.1 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Working dir: /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp > > Command line: > >gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter > -ignh -merge interactive > > > > > > > > > > --- > > Program: gmx pdb2gmx, version 2018.1 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) > > Function:void gmx::CommandLineParser::parse(int*, char**) > > > > > > Error in user input: > > Invalid command-line options > >In command-line option -water > > Invalid value: tip4pd > > > > > > > > > > > > > > > > -- Original -- > > From: "ZHANG Cheng"<272699...@qq.com>; > > Date: Fri, Jan 11, 2019 00:31 AM > > To: "gromacs.org_gmx-users"; > > > > Subject: Re: Why pdb2gmx could not accept tip4pd as the water model? > > > > > > > > Thank you Justin. > > > > > > The "watermodels.dat" and "tip4pd.itp" are already in the ff > subdirectory. > > > > > > The "watermodels.dat" content is: > > tip4pd TIP4P-D TIP 4-point with increased dispersion > > > > > > But "-water tip4pd" still has the error. > > > > > > -- Original -- > > From: "ZHANG Cheng"<272699...@qq.com>; > > Date: Fri, Jan 11, 2019 00:12 AM > > To: "gromacs.org_gmx-users"; > > > > Subject: Why pdb2gmx could not accept tip4pd as the water model? > > > > > > > > I got the a99SB-disp forcefield with tip4pd.itp as the water model. > > > > > > The a99SB-disp.ff file has been copied: > "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" > > The tip4pd.itp file has also been copied to > "/usr/local/gromacs/share/gromacs/top" > > > > > > However using "-water tip4pd" in "pdb2gmx" will cause error: > > > > > > Error in user input: > > Invalid command-line options > >In command-line option -water > > Invalid value: tip4pd > > > > > > > > So how can I properly use the tip4pd in "pdb2gmx"? > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] RMSD plots protein-peptide complex
Ok I understand. We create index groups for backbone atoms of selected protein only. I made index group for whole residues of selected protein. Will do again. Ok then let us see. On Fri, 11/1/19, Justin Lemkul wrote: Subject: Re: [gmx-users] RMSD plots protein-peptide complex To: gmx-us...@gromacs.org Date: Friday, 11 January, 2019, 1:56 AM On 1/10/19 8:23 PM, Dr. Seema Mishra wrote: > Ok so I created index group already and fed it ti trjconv and g_rms. But while selecting atoms in g_rms stage if we select 22 (for index group) then all atoms of index group will be selected. We want inly backbone atoms of index group. I thought my commands just written before here would work. Otherwise, How to get that? Like I said before, you need to create an index group that has the atoms you want to analyze. I don't know what group 22 is and you're not posting complete information. If you want the backbone of the protein (receptor), then create an index group with just those atoms so you can use it for analysis. -Justin > > On Thu, 10/1/19, Justin Lemkul wrote: > > Subject: Re: [gmx-users] RMSD plots protein-peptide complex > To: gmx-us...@gromacs.org > Date: Thursday, 10 January, 2019, 4:19 PM > > > > On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: > > > > Thanks Justin. > > Are these two commands for RMSD OK after > making index groups for protein only? Forgive my > silliness: > > gmx trjconv -s md_0_1.tpr -f > md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur > compact > > Select 0 > > > > gmx rms -s md_0_1.tpr > -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns > > > > Select 4 4 for > backbone atoms. I think then GROMACS will recognize only the > index groups will be used for identifying backbones > > > > Sure, > GROMACS does what you tell it. If you choose the default > group 4 > (Backbone), it will consider all > atoms that qualify as backbone, > encompassing any protein in the system. What > you need to do is create an > index group > with only the relevant atoms of the protein receptor (not > > the peptide ligand) and use that group for > analysis. The mere presence > of a > protein-only index group will do nothing for you; you need > to > actually use it. > > -Justin > > > > > On Wednesday, 9 > January, 2019, 8:30:52 PM IST, Justin Lemkul > wrote: > > > > > > > > On 1/9/19 6:07 AM, > Dr. Seema Mishra wrote: > >> Hello > >> Any idea how to generate RMSD plots > for only the protein in a protein-peptide complex? I mean, > do give me commands for using only the protein backbone > atoms as the g_rmsd uses all backbone atoms of peptide as > well and I do not want peptide RMSD plots included. > > Make an index group that includes only the > atoms you want to analyze. > > > > -Justin > > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 > Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of > Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu > | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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-requ...@gromacs.org. > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@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
Re: [gmx-users] RMSD plots protein-peptide complex
On 1/10/19 8:23 PM, Dr. Seema Mishra wrote: Ok so I created index group already and fed it ti trjconv and g_rms. But while selecting atoms in g_rms stage if we select 22 (for index group) then all atoms of index group will be selected. We want inly backbone atoms of index group. I thought my commands just written before here would work. Otherwise, How to get that? Like I said before, you need to create an index group that has the atoms you want to analyze. I don't know what group 22 is and you're not posting complete information. If you want the backbone of the protein (receptor), then create an index group with just those atoms so you can use it for analysis. -Justin On Thu, 10/1/19, Justin Lemkul wrote: Subject: Re: [gmx-users] RMSD plots protein-peptide complex To: gmx-us...@gromacs.org Date: Thursday, 10 January, 2019, 4:19 PM On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: > > Thanks Justin. > Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: > gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact > Select 0 > > gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns > > Select 4 4 for backbone atoms. I think then GROMACS will recognize only the index groups will be used for identifying backbones > Sure, GROMACS does what you tell it. If you choose the default group 4 (Backbone), it will consider all atoms that qualify as backbone, encompassing any protein in the system. What you need to do is create an index group with only the relevant atoms of the protein receptor (not the peptide ligand) and use that group for analysis. The mere presence of a protein-only index group will do nothing for you; you need to actually use it. -Justin > > On Wednesday, 9 January, 2019, 8:30:52 PM IST, Justin Lemkul wrote: > > > > On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: >> Hello >> Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. > Make an index group that includes only the atoms you want to analyze. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
On 1/10/19 11:51 AM, ZHANG Cheng wrote: I think using "-water tip4pd" will always cause errors, without allowing me to select the forcefield. I also put the ff directory to my launching folder, but still the same problem. Simply using "-water tip4p" will allow me to select the forcefield. But I want to use tip4pd, not tip4p. Turns out you'll have to make the selection interactively or otherwise change the pdb2gmx source code to allow for a new water model to be selected. -Justin The below is the error message. GROMACS: gmx pdb2gmx, version 2018.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp Command line: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter -ignh -merge interactive --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:31 AM To: "gromacs.org_gmx-users"; Subject: Re: Why pdb2gmx could not accept tip4pd as the water model? Thank you Justin. The "watermodels.dat" and "tip4pd.itp" are already in the ff subdirectory. The "watermodels.dat" content is: tip4pd TIP4P-D TIP 4-point with increased dispersion But "-water tip4pd" still has the error. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: Why pdb2gmx could not accept tip4pd as the water model? I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] gromacs 2016.3 solvate error for methanol water mixture - bug?
On 1/10/19 11:35 AM, Hermann, Johannes wrote: Hi Justin, I did not upgrade to version 2018. So I do not know. If you can, please try it, as neither the 5.1.x nor the 2016.x series is receiving bug fixes like these. -Justin All the best Johannes On 10.01.19 17:19, Justin Lemkul wrote: On 1/10/19 9:47 AM, Hermann, Johannes wrote: Dear all, I "solved" the issue and want to share it with you in case someone runs in the same trouble. Unfortunately for me it seems like a bug: When I use my old gromacs version 5.1.4 the command works just fine. Does the problem persist in version 2018 or 2019? -Justin All the best Johannes On 09.01.19 16:44, Hermann, Johannes wrote: Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: *** Error in `gmx_mpi': free(): invalid pointer: 0x0364d1c0 *** Has anyone experienced this before? Has anyone a suggestion what might have gone wrong? Thank you very much in advance. All the best Johannes __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] RMSD plots protein-peptide complex
Ok so I created index group already and fed it ti trjconv and g_rms. But while selecting atoms in g_rms stage if we select 22 (for index group) then all atoms of index group will be selected. We want inly backbone atoms of index group. I thought my commands just written before here would work. Otherwise, How to get that? On Thu, 10/1/19, Justin Lemkul wrote: Subject: Re: [gmx-users] RMSD plots protein-peptide complex To: gmx-us...@gromacs.org Date: Thursday, 10 January, 2019, 4:19 PM On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: > > Thanks Justin. > Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: > gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact > Select 0 > > gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns > > Select 4 4 for backbone atoms. I think then GROMACS will recognize only the index groups will be used for identifying backbones > Sure, GROMACS does what you tell it. If you choose the default group 4 (Backbone), it will consider all atoms that qualify as backbone, encompassing any protein in the system. What you need to do is create an index group with only the relevant atoms of the protein receptor (not the peptide ligand) and use that group for analysis. The mere presence of a protein-only index group will do nothing for you; you need to actually use it. -Justin > > On Wednesday, 9 January, 2019, 8:30:52 PM IST, Justin Lemkul wrote: > > > > On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: >> Hello >> Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. > Make an index group that includes only the atoms you want to analyze. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] RDF in gromacs
What is the selection syntax you are actually using? Copy and paste, don't do from memory. On Wed, 9 Jan. 2019, 8:40 pm daniel madulu shadrack Hi, > I am calculating the rdf of my system as follows. > > 1. rdf of oxygen atom of my drug and water this is successful (I just made > an index file and for water i choose eg. 5 & a OW) this worked fine. > > 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the > hydroxyl group of the chitosan, I am getting difficult on how to select > only oxygen in chitosan or polymer and make an index file, I am getting > syntax errors, How should I do? > > Help. > > -- > > > *Regards, * > Daniel Madulu Shadrack., (M.Sc. Chem). > PhD Research Scholar > (Nanomedicine & Comp. Aided Drug Design) > > dmss...@gmail.com > - > *FOR GOD LET US DO MUCH, **QUICK AND **WELL*.. > *St. Gaspar Del Bufalo* > -- > 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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] Dihedral restraints
Hi, Or provide feedback to CHARMM-GUI people! Mark On Thu., 10 Jan. 2019, 17:22 Justin Lemkul, wrote: > > > On 1/10/19 10:51 AM, ABEL Stephane wrote: > > Thank you Mark, > > > > With your example, I have finally resolved my problem and finally found > that the dihedral restraints were not actived in my simulations :(( > > > > If someone is interested to know how I did for resolving my problem > especially when you use the files generated by CHARMM-GUI for GROMACS, do > not hesitate to contact me directly > > Posting directly to the list with your solution would be greatly > appreciated, so that when someone Googles this same question in the > future, they will immediately have their answer. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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-requ...@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-requ...@gromacs.org.
[gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M
Hello dear users, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found ( https://plumed.github.io/doc-v2.4/user-doc/html/hrex.html) explicitly say that it will not work with CHARMM cmap. Thus, I was wondering if anyone knows an alternative method of run REST2 simulations in GROMACS in general or how to solve the cmap problem mentioned in the instructions. Thank you in advance, Aram -- 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-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
I think using "-water tip4pd" will always cause errors, without allowing me to select the forcefield. I also put the ff directory to my launching folder, but still the same problem. Simply using "-water tip4p" will allow me to select the forcefield. But I want to use tip4pd, not tip4p. The below is the error message. GROMACS: gmx pdb2gmx, version 2018.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp Command line: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter -ignh -merge interactive --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function:void gmx::CommandLineParser::parse(int*, char**) Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:31 AM To: "gromacs.org_gmx-users"; Subject: Re: Why pdb2gmx could not accept tip4pd as the water model? Thank you Justin. The "watermodels.dat" and "tip4pd.itp" are already in the ff subdirectory. The "watermodels.dat" content is: tip4pd TIP4P-D TIP 4-point with increased dispersion But "-water tip4pd" still has the error. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: Why pdb2gmx could not accept tip4pd as the water model? I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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-requ...@gromacs.org.
Re: [gmx-users] gromacs 2016.3 solvate error for methanol water mixture - bug?
Hi Justin, I did not upgrade to version 2018. So I do not know. All the best Johannes On 10.01.19 17:19, Justin Lemkul wrote: On 1/10/19 9:47 AM, Hermann, Johannes wrote: Dear all, I "solved" the issue and want to share it with you in case someone runs in the same trouble. Unfortunately for me it seems like a bug: When I use my old gromacs version 5.1.4 the command works just fine. Does the problem persist in version 2018 or 2019? -Justin All the best Johannes On 09.01.19 16:44, Hermann, Johannes wrote: Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: *** Error in `gmx_mpi': free(): invalid pointer: 0x0364d1c0 *** Has anyone experienced this before? Has anyone a suggestion what might have gone wrong? Thank you very much in advance. All the best Johannes __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
Thank you Justin. The "watermodels.dat" and "tip4pd.itp" are already in the ff subdirectory. The "watermodels.dat" content is: tip4pd TIP4P-D TIP 4-point with increased dispersion But "-water tip4pd" still has the error. -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:12 AM To: "gromacs.org_gmx-users"; Subject: Why pdb2gmx could not accept tip4pd as the water model? I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
On 1/10/19 11:12 AM, ZHANG Cheng wrote: I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? The water model must appear in watermodels.dat within the force field subdirectory, and the corresponding .itp file must also be in the force field subdirectory, not in $GMXLIB. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] Dihedral restraints
On 1/10/19 10:51 AM, ABEL Stephane wrote: Thank you Mark, With your example, I have finally resolved my problem and finally found that the dihedral restraints were not actived in my simulations :(( If someone is interested to know how I did for resolving my problem especially when you use the files generated by CHARMM-GUI for GROMACS, do not hesitate to contact me directly Posting directly to the list with your solution would be greatly appreciated, so that when someone Googles this same question in the future, they will immediately have their answer. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] gromacs 2016.3 solvate error for methanol water mixture - bug?
On 1/10/19 9:47 AM, Hermann, Johannes wrote: Dear all, I "solved" the issue and want to share it with you in case someone runs in the same trouble. Unfortunately for me it seems like a bug: When I use my old gromacs version 5.1.4 the command works just fine. Does the problem persist in version 2018 or 2019? -Justin All the best Johannes On 09.01.19 16:44, Hermann, Johannes wrote: Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: *** Error in `gmx_mpi': free(): invalid pointer: 0x0364d1c0 *** Has anyone experienced this before? Has anyone a suggestion what might have gone wrong? Thank you very much in advance. All the best Johannes __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] RMSD plots protein-peptide complex
On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: Thanks Justin. Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact Select 0 gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns Select 4 4 for backbone atoms. I think then GROMACS will recognize only the index groups will be used for identifying backbones Sure, GROMACS does what you tell it. If you choose the default group 4 (Backbone), it will consider all atoms that qualify as backbone, encompassing any protein in the system. What you need to do is create an index group with only the relevant atoms of the protein receptor (not the peptide ligand) and use that group for analysis. The mere presence of a protein-only index group will do nothing for you; you need to actually use it. -Justin On Wednesday, 9 January, 2019, 8:30:52 PM IST, Justin Lemkul wrote: On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. Make an index group that includes only the atoms you want to analyze. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
Re: [gmx-users] Free energy calculation of Histone
On 1/10/19 2:17 AM, Mark Abraham wrote: Hi, That's the wrong way around. :-) One doesn't do a lab experiment first and then decide what you wanted to observe from it, to either :-). There are tutorials for computing free energy of solvation, which I suggest you follow, and I suspect your fully solvated simulation won't be useful for that. Note, however, that the alchemical approach that most tutorials use would never converge for something as large as a histone, let alone even a moderately sized polypeptide. MM/PBSA post-processing might be useful, but the values will be astronomical, as would (likely) the error bars. -Justin Mark On Thu., 10 Jan. 2019, 02:45 Ayesha Kanwal, wrote: Dear all users, I am new for using GROMACS. and also read the tutorial of Methane and water. I have already simulated data of 100 ns for four histones. I want to know how to calculate free energy solvation from this data. which topology file and coordinate files I will use? I will appreciate your good suggestions. Regards Ayesha -- 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-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@gromacs.org.
[gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
I got the a99SB-disp forcefield with tip4pd.itp as the water model. The a99SB-disp.ff file has been copied: "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff" The tip4pd.itp file has also been copied to "/usr/local/gromacs/share/gromacs/top" However using "-water tip4pd" in "pdb2gmx" will cause error: Error in user input: Invalid command-line options In command-line option -water Invalid value: tip4pd So how can I properly use the tip4pd in "pdb2gmx"? -- 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-requ...@gromacs.org.
Re: [gmx-users] Dihedral restraints
Thank you Mark, With your example, I have finally resolved my problem and finally found that the dihedral restraints were not actived in my simulations :(( If someone is interested to know how I did for resolving my problem especially when you use the files generated by CHARMM-GUI for GROMACS, do not hesitate to contact me directly Thanks again Stéphane -- Message: 1 Date: Thu, 10 Jan 2019 07:20:26 +0100 From: Mark Abraham To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Dihedral restraints Message-ID: Content-Type: text/plain; charset="UTF-8" Hi, You can see a working example at https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log so I conclude that your restraints are inactive, somehow. Please check your include statements, etc. Mark On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, wrote: > Thanks Mark for your reply > > In the log and edr files I only see an "Position Rest." term. So do you > mean that the contributions on the dihedral restrains is added in in total > energy without additional terms in the energy output in log file and the > edr ? > > Thank you in advance for the clarification. > > St?phane > > > -- > > Message: 3 > Date: Wed, 9 Jan 2019 12:32:31 +0100 > From: Mark Abraham > To: gmx-us...@gromacs.org > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] Dihedral restraints > Message-ID: > xv8qbic+t1h1cwwcnkisdfxnoja7xbot...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > IIRC that's enough, for dihedral restraints. You will see energy > contributions from the the restraints appear in your .log and .edr files if > the restraints are active. I don't recall if there is anything printed by > mdrun before the simulation commences. > > Mark > > On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane > wrote: > > > Hello > > > > I would like to apply some dihedral restraints in different residues of > my > > protein during the production stage. For that I have added at the end of > > the protein itp the section > > [ dihedral_restraints ]. Is it enough ? Should I add something else in > the > > mdp ? In other words, how to be sure that the restraints are effectively > > applied during the run ? > > > > I am using GROMACS 2018.2 > > > > Thank in advance and happy new year to all > > > > St?phane > > -- > -- > 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-requ...@gromacs.org. > -- Message: 2 Date: Thu, 10 Jan 2019 07:20:26 +0100 From: Mark Abraham To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] Dihedral restraints Message-ID: Content-Type: text/plain; charset="UTF-8" Hi, You can see a working example at https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log so I conclude that your restraints are inactive, somehow. Please check your include statements, etc. Mark On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, wrote: > Thanks Mark for your reply > > In the log and edr files I only see an "Position Rest." term. So do you > mean that the contributions on the dihedral restrains is added in in total > energy without additional terms in the energy output in log file and the > edr ? > > Thank you in advance for the clarification. > > St?phane > > > -- > > Message: 3 > Date: Wed, 9 Jan 2019 12:32:31 +0100 > From: Mark Abraham > To: gmx-us...@gromacs.org > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] Dihedral restraints > Message-ID: > xv8qbic+t1h1cwwcnkisdfxnoja7xbot...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > IIRC that's enough, for dihedral restraints. You will see energy > contributions from the the restraints appear in your .log and .edr files if > the restraints are active. I don't recall if there is anything printed by > mdrun before the simulation commences. > > Mark > > On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane > wrote: > > > Hello > > > > I would like to apply some dihedral restraints in different residues of > my > > protein during the production stage. For that I have added at the end of > > the protein itp the section > > [ dihedral_restraints ]. Is it enough ? Should I add something else in > the > > mdp ? In other words, how to be sure that the restraints are effectively > > applied during the run ? > > > > I am using GROMACS 2018.2 > > > > Thank in advance and
[gmx-users] Another last-minute GROMACS job opportunity: Closing Fri Jan 11 :-)
Hi! Some of you might have seen the open position for GROMACS development last fall, but KTH in Stockholm actually has another job opportunity for somebody who would be interested in working more on user outreach, helping with support and working with grand challenges for Exascale systems. This is part of a larger joint EU Center-of-Excellence, so the person will be working in the same place as the rest of the GROMACS team in our lab, and there will be opportunities to also engage in code development and application research projects. However, there is *ONE* caveat: The closing date is already tomorrow (Fri, Jan 11)! The rules are quite strict around the closing date, so if you (or someone you know) has any interest whatsoever, please submit your application through the KTH electronic system mentioned in the job ad (we are not allowed to consider applications submitted late or directly to us by email)! Here's a link to the job ad: https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:238941/where:4/ All the best, Erik -- Erik Lindahl Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University Science for Life Laboratory, Box 1031, 17121 Solna, Sweden -- 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-requ...@gromacs.org.
Re: [gmx-users] Status of GROMACS native Windows Builds
Hi, Great. If you use e.g. a tarball from https://gerrit.gromacs.org/#/c/8948/ then I hope that the std::max issue will be fixed (but you still need the other workarounds) Mark On Thu, Jan 10, 2019 at 3:38 PM Wahab Mirco < mirco.wa...@chemie.tu-freiberg.de> wrote: > Hi Mark, > > thanks for your reply. > > On 10.01.2019 12:02, Mark Abraham wrote: > >> -- Check for working NVCC/C compiler combination - broken > >>> CMake Error at cmake/gmxManageNvccConfig.cmake:185 (message): > >>> CUDA compiler does not seem to be functional. > >>> Call Stack (most recent call first): > >>> cmake/gmxManageGPU.cmake:204 (include) > >>> CMakeLists.txt:590 (gmx_gpu_setup) > >>> > >> > > This check isn't functional on Windows, but nvcc might be. Please try > > setting cmake -DGMX_NVCC_WORKS=1 for now, and see how you go. I have > > proposed a fix for 2019.1 that will stop trying to make this check. > > > > This option works for cmake, leading to the compilation error (similar > error as with OpenCL) with VC's std::max (): > > 7>Building NVCC (Device) object > > src/gromacs/CMakeFiles/libgromacs.dir/ewald/Release/libgromacs_generated_pme-gpu-internal.cpp.obj > 7>pme-gpu-internal.cpp > 7>D:/LibSrc/Gromacs2019/gromacs-2019/src/gromacs/ewald/pme-gpu-internal.cpp(1135): > > error : no instance of overloaded function "std::max" matches the > argument list > 7>argument types are: (unsigned long long, unsigned long) > 7> > > So, GROMACS 2019 + CUDA on Windows appears close! Maybe I can > look into the sources on the weekend if I got some spare time. > > Thanks & regards > > M. > -- > 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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] gromacs 2016.3 solvate error for methanol water mixture - bug?
Dear all, I "solved" the issue and want to share it with you in case someone runs in the same trouble. Unfortunately for me it seems like a bug: When I use my old gromacs version 5.1.4 the command works just fine. All the best Johannes On 09.01.19 16:44, Hermann, Johannes wrote: Dear gromacs-users, I generated and equilibrated a box (4 x 4 x 4 nm) containing a mixture of water and methanol. With this I wanted to solvate my protein: gmx solvate -cp protein.gro -cs wat-methanol.gro -o prot_solv.gro -p topol.top However, this results in an error starting with: *** Error in `gmx_mpi': free(): invalid pointer: 0x0364d1c0 *** Has anyone experienced this before? Has anyone a suggestion what might have gone wrong? Thank you very much in advance. All the best Johannes __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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-requ...@gromacs.org.
Re: [gmx-users] Status of GROMACS native Windows Builds
Hi Mark, thanks for your reply. On 10.01.2019 12:02, Mark Abraham wrote: >> -- Check for working NVCC/C compiler combination - broken >>> CMake Error at cmake/gmxManageNvccConfig.cmake:185 (message): >>> CUDA compiler does not seem to be functional. >>> Call Stack (most recent call first): >>> cmake/gmxManageGPU.cmake:204 (include) >>> CMakeLists.txt:590 (gmx_gpu_setup) >>> >> > This check isn't functional on Windows, but nvcc might be. Please try > setting cmake -DGMX_NVCC_WORKS=1 for now, and see how you go. I have > proposed a fix for 2019.1 that will stop trying to make this check. > This option works for cmake, leading to the compilation error (similar error as with OpenCL) with VC's std::max (): 7>Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/ewald/Release/libgromacs_generated_pme-gpu-internal.cpp.obj 7>pme-gpu-internal.cpp 7>D:/LibSrc/Gromacs2019/gromacs-2019/src/gromacs/ewald/pme-gpu-internal.cpp(1135): error : no instance of overloaded function "std::max" matches the argument list 7>argument types are: (unsigned long long, unsigned long) 7> So, GROMACS 2019 + CUDA on Windows appears close! Maybe I can look into the sources on the weekend if I got some spare time. Thanks & regards M. -- 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-requ...@gromacs.org.
Re: [gmx-users] RMSD plots protein-peptide complex
Thanks Justin. Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact Select 0 gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns Select 4 4 for backbone atoms. I think then GROMACS will recognize only the index groups will be used for identifying backbones On Wednesday, 9 January, 2019, 8:30:52 PM IST, Justin Lemkul wrote: On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: > Hello > Any idea how to generate RMSD plots for only the protein in a protein-peptide > complex? I mean, do give me commands for using only the protein backbone > atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not > want peptide RMSD plots included. Make an index group that includes only the atoms you want to analyze. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] Status of GROMACS native Windows Builds
Hi, On Wed, Jan 9, 2019 at 5:28 PM Mark Abraham wrote: > Hi, > > On Wed, Jan 9, 2019 at 4:54 PM Wahab Mirco < > mirco.wa...@chemie.tu-freiberg.de> wrote: > >> The build machine also has an old GTX-680 4GB with working CUDA 10 and >> > working OpenCL 1.2. Neither a Cuda-Build nor an OpenCL build would >> succeed (see Appendix). >> >> Q: is further support for the windows platform to be expected? >> > > Our major interests are the extra portability ensured by supporting MSVC > and its different C++ standard library. And later probably the Microsoft > correctness checking machinery, e.g. for the GSL. > > We'd be likely to accept patches that would get the GPU support working, > but we won't prioritize effort to do it ourselves. Some of the type > mismatches look worth fixing on general principles, and e.g. if clFFT > doesn't support Windows, then we should fix our build stuff. I opened an > issue in our tracker. > > Thanks! > > Mark > > Thanks & Regards >> >> M. >> >> >> --- >> >> Appendix: >> >> CUDA: cmake (3.13.2) would fail creating a makefile by complaining: >> >> -- Check for working NVCC/C compiler combination >> CMake Error at cmake/gmxManageNvccConfig.cmake:180 (message): >>message called with incorrect number of arguments >> Call Stack (most recent call first): >>cmake/gmxManageGPU.cmake:204 (include) >>CMakeLists.txt:590 (gmx_gpu_setup) >> > I proposed a fix for that for 2019.1. > -- Check for working NVCC/C compiler combination - broken >> CMake Error at cmake/gmxManageNvccConfig.cmake:185 (message): >>CUDA compiler does not seem to be functional. >> Call Stack (most recent call first): >>cmake/gmxManageGPU.cmake:204 (include) >>CMakeLists.txt:590 (gmx_gpu_setup) >> > This check isn't functional on Windows, but nvcc might be. Please try setting cmake -DGMX_NVCC_WORKS=1 for now, and see how you go. I have proposed a fix for 2019.1 that will stop trying to make this check. > OpenCL: cmake detects OpenCL 1.2 and creates a makefile, but compilation >> fails at several places: >> >> 1>fft_binary_lookup.cpp >> 1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(123): >> >> error C2664: 'HANDLE >> CreateFileA(LPCSTR,DWORD,DWORD,LPSECURITY_ATTRIBUTES,DWORD,DWORD,HANDLE)': >> >> cannot convert argument 1 from 'const _Elem *' to 'LPCSTR' >> 1>with >> 1>[ >> 1>_Elem=wchar_t >> 1>] >> 1>D:\LibSrc\Gromacs2019\gromacs-2019\src\external\clFFT\src\library\fft_binary_lookup.cpp(129): >> >> note: Types pointed to are unrelated; conversion requires >> reinterpret_cast, C-style cast or function-style cast >> 1>Done building project "clFFT.vcxproj" -- FAILED. >> 2 >> > Unfortunately clFFT doesn't support recent versions of MSVC, so unless you make an install of their library that GROMACS will find (see https://github.com/clMathLibraries/clFFT/releases), there is no way to build GROMACS with OpenCL support, as that requires clFFT. Or try GROMACS 2018.x! (I proposed a fix for our build system here too.) and >> >> 2>D:\LibSrc\Gromacs2019\gromacs-2019\src\gromacs\ewald\pme-gpu-internal.cpp(1135): >> >> > I also proposed a code fix for this one. Thanks! Mark -- 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-requ...@gromacs.org.
[gmx-users] Problem w.r.t simulation with a Heme containing protein
Dear all, I have tried to process the heme containing protein using GROMOS 54a7. Although I am able to convert the pro.pdb to pro.gro, I am getting a warning sign, like this, -- While running pdb2gmx -f pro.pdb -o pro.gro . . . Before cleaning: 9225 pairs Before cleaning: 11318 dihedrals Making cmap torsions... There are 3062 dihedrals, 3024 impropers, 8613 angles 9225 pairs, 5884 bonds and 0 virtual sites Total mass 63413.819 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'A' (43 atoms, 1 residues) Warning: Starting residue HEM605 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HEM605 HEM605 CAB20 CAC27 HEM605 CAC27 0.815 HEM605Fe43 0.582 0.570 Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 47 atoms Chain time... Making bonds... Number of bonds was 54, now 54 Generating angles, dihedrals and pairs... Before cleaning: 15 pairs Before cleaning: 154 dihedrals Making cmap torsions... There are 20 dihedrals, 46 impropers, 102 angles 15 pairs, 54 bonds and 0 virtual sites Total mass 614.485 a.m.u. Total charge -2.000 e Writing topology Including chain 1 in system: 5752 atoms 552 residues Including chain 2 in system: 47 atoms 1 residues Now there are 5799 atoms and 553 residues Total mass in system 64028.304 a.m.u. Total charge in system -3.000 e - And when I try to add ions using grompp and ions.mdp i get this... NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 1795342617 Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file topol_Other_chain_A2.itp, line 162]: No default G96Angle types ERROR 2 [file topol_Other_chain_A2.itp, line 164]: No default G96Angle types ERROR 3 [file topol_Other_chain_A2.itp, line 167]: No default G96Angle types ERROR 4 [file topol_Other_chain_A2.itp, line 169]: No default G96Angle types ERROR 5 [file topol_Other_chain_A2.itp, line 172]: No default G96Angle types ERROR 6 [file topol_Other_chain_A2.itp, line 174]: No default G96Angle types ERROR 7 [file topol_Other_chain_A2.itp, line 177]: No default G96Angle types ERROR 8 [file topol_Other_chain_A2.itp, line 179]: No default G96Angle types -- Could you please suggest a solution. Would it help, if i added the following line to residues.dat in $gmx$ --- . . IB+Ion HEM Protein -- Regards, Prasanth. -- 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-requ...@gromacs.org.
