> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Charges and Antechamber (ABEL Stephane) > 2. Re: peptide ligand (farial tavakoli) > 3. Re: grompp very slow generating .tpr when excluded bonded > neighbours is large (Mark Abraham) > 4. Re: Charges and Antechamber (Jo?o Henriques) > 5. checking simulation progress (Bukunmi Akinwunmi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Oct 2017 15:10:33 +0000 > From: ABEL Stephane <stephane.a...@cea.fr> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] Charges and Antechamber > Message-ID: > <3e39b768bb199548ab18f7289e7534af38818...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="us-ascii" > > HI > > It is quite easy to derive RESP charges and use them with GROMACS. You > could follow the steps > > 1) Build a pdb file of your molecule/modified residue > 2) Use the web server pyRED > (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive > the RESP charges. The webserver will also give you all the necessary > parameters of the ff (mol2 file, atom types, (non)bonded parameters) > 3) Use these parameters to construct a rtp file for GROMACS for a given > force field > 4) and finally use pdb2gmx with the pdb file to obtain the itp file. > > That's all > > Good luck > > > ------------------------------ > > Message: 2 > Date: Tue, 3 Oct 2017 15:13:58 +0000 (UTC) > From: farial tavakoli <farial.tavak...@ymail.com> > To: <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] peptide ligand > Message-ID: <1201432437.876905.1507043638...@mail.yahoo.com> > Content-Type: text/plain; charset=UTF-8 > > blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px > #715FFA solid !important; padding-left:1ex !important; > background-color:white !important; } Thanks alot for your advxe > I would really appreciate if you advice me more to split protein and > ligand in index file, I saw the index help , but couldnt find out how > should I use ? ?splitch? nr ? script to split them.? > With best regardsFarial
gmx make_ndx -f em.gro -o index.ndx then select protein ( in your case it will contain both the protein and the peptide) and your ligand. press q (save it) now assemble your nvt tpr file using grompp ( pass here -n index.ndx) It is explained very nicely in gromacs tutorial Protein - Ligand (Equilibration section) thank you > > Sent from Yahoo Mail for iPhone > > > On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalem...@vt.edu> > wrote: > > > > On 10/3/17 9:17 AM, ?farial tavakoli? ? wrote: >> Dear Justin >> >> Thank you so much for your reply. >> You mean , I should generate a topology file for my complex instead of >> creating topology for each of them separately ? >> > > As long as the protein and peptide ligand are denoted as being in > separate chains (different chain ID or use of TER in the PDB file), then > pdb2gmx will do everything for you. > > -Justin > >> >> >> ------------------------------------------------------------------------ >> *From:* Justin Lemkul <jalem...@vt.edu> >> *To:* gmx-us...@gromacs.org; ?farial tavakoli? ? >> <farial.tavak...@ymail.com> >> *Sent:* Tuesday, 3 October 2017, 16:35:49 >> *Subject:* Re: [gmx-users] peptide ligand >> >> >> >> On 10/3/17 4:26 AM, ?farial tavakoli? ? wrote: >> > Dear GROMACS users >> > I need to run a MD on my Protein-peptide ligand complex in GROMACS. >> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes] >> was Protein_chain_B) and converted it to .itp file to string it in >> Protein.top file, then, added Protein_chain_B in [ molecules ] >> directive to create one topology file for my complex. Created newbox >> and solvate. >> >> You shouldn't have to do any topology manipulation. pdb2gmx handles >> multiple >> chains natively without any additional effort on your part. >> >> -Justin >> >> >> > But when I gave this command:gmx grompp -f em_real.mdp -c >> solv_ions.gro -p topol.top -o em.tpr >> > >> > I faced to this error: >> > >> > Group Protein_chain_B referenced in the .mdb file was not found in >> the index file. Group names must match either [moleculetype] names or >> custom index group names, in which case you must supply an index file >> to the '-n' option >> > of grompp. >> > >> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is >> Protein_chain_B , but GROMACS gives error. >> > Would you please advice me how can I solve this problem? >> > >> > Best >> > Farial >> >> > >> > >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu <mailto:jalem...@vt.edu> | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> >> ================================================== >> >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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: 3 > Date: Tue, 03 Oct 2017 15:37:31 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] grompp very slow generating .tpr when > excluded bonded neighbours is large > Message-ID: > <camnumatwcxnmaxv7wxrhjnh6o-nz9vkpxvwto41n+9mi8kj...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > I'm sure we have opportunities to improve this code - please do file a > redmine issue with repro inputs so we can profile and see! > > Thanks, > > Mark > > On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 10/2/17 11:14 PM, Dallas Warren wrote: >> > Thanks for the reply Justin. >> > >> > I am just going to use the largest exclusion bond distance I can, then >> > ignore the RDF of those beyond that distance. >> > >> > Seems curious to me (not actually understanding what grommp is >> > generating) that the list is so large. These are linear molecules, 38 >> > atoms, 60 molecules in total. >> >> It generates a matrix of all possible exclusions, sorts them, then >> removes >> duplicates. So for nrexcl = 37 you need memory on the order of 37 * 37 * >> 60 * (2 >> * sizeof(int)) - the factor of 2 for the atom numbers comes from the >> fact >> that >> you're actually allocating an array of type "sortable" which is a pair >> of >> atom >> numbers. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Virginia Tech Department of Biochemistry >> >> 303 Engel Hall >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >> >> ================================================== >> -- >> 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: 4 > Date: Tue, 3 Oct 2017 17:41:27 +0200 > From: Jo?o Henriques <joao.m.a.henriq...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Charges and Antechamber > Message-ID: > <CAHv45qPTFJMwRjoXxBYU-EGxU6toR2ZmZWq=7eq14gc9v_a...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Or this... :) I've never used it, but I'm sure it works like a charm. I > personally prefer to be more involved in all stages of the process, but > I'm > a bit old school and I like to avoid "black boxes" for my own learning > benefit. That being said, I'm sure it does the job and it's faster & > simpler. It's probably the best way to go for someone with less experience > with this sort of task. > > Cheers, > > J > > On Oct 3, 2017 5:10 PM, "ABEL Stephane" <stephane.a...@cea.fr> wrote: > > HI > > It is quite easy to derive RESP charges and use them with GROMACS. You > could follow the steps > > 1) Build a pdb file of your molecule/modified residue > 2) Use the web server pyRED (http://upjv.q4md- > forcefieldtools.org/REDServer-Development/) and derive the RESP charges. > The webserver will also give you all the necessary parameters of the ff > (mol2 file, atom types, (non)bonded parameters) > 3) Use these parameters to construct a rtp file for GROMACS for a given > force field > 4) and finally use pdb2gmx with the pdb file to obtain the itp file. > > That's all > > Good luck > -- > 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: 5 > Date: Tue, 3 Oct 2017 16:03:01 +0000 > From: Bukunmi Akinwunmi <bukunmi.akinwu...@uef.fi> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] checking simulation progress > Message-ID: > > <he1pr01mb2940456c37826a4807aaae1385...@he1pr01mb2940.eurprd01.prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > dear gmx-users, > my simulation has been running for sometime but now I want to know how > long is left for the simulation to be completed. I need help with the > command to analyse a running simulation. > > Best regards, > Bukunmi > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 162, Issue 7 > ***************************************************** > * * * 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.
