Hi Chandran, What did you try, and what error did it come up with? What platform are you using, and which version of DSSP? The latest version of DSSP won't work with Gromacs yet.
Cheers, Tsjerk On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran <ckaru2...@yahoo.com> wrote: > Dear ALL, > > We could not run DSSP for analysing the secondary structure. Any > help in this regard is very much appreciated > > > *******************************+ > Dr.Karunakaran Chandran + > Biophysics Department + > Medical College of Wisconsin + > Milwaukee, WI-53226 + > Resi.: 414-443-0085 + > Off : 414-456-4034 + > ******************************** > ________________________________ > From: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org> > To: gmx-users@gromacs.org > Sent: Monday, 19 March 2012 4:30 PM > Subject: gmx-users Digest, Vol 95, Issue 125 > > 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. Editing potential parameters (Asaf Farhi) > 2. nrexcl in topology (Lara Bunte) > 3. extending simulation (priya thiyagarajan) > 4. Re: nrexcl in topology (R.Perez Garcia) > 5. Re: Force constant - Umbrella Sampling (lloyd riggs) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 19 Mar 2012 10:06:47 +0000 > From: Asaf Farhi <asaf.fa...@weizmann.ac.il> > Subject: [gmx-users] Editing potential parameters > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: <7D02BCA1E8377E4AABC2E8F59B6D0CDA09E25B@IBWMBX01> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gromacs user > > Hi. My name is Asaf and I'm trying to edit potential parameters for the non > bonded interaction potential terms between specific atoms (k1 for 1 subset > of pairs and k2 for anoother subset of pairs). > Is the pairs section in the topology file the correct place to do this? and > if so how would you incorporate spring constant for particular pair > interaction? > > Many thanks. > Best regards, > Asaf > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/6adac179/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 19 Mar 2012 10:19:22 +0000 (GMT) > From: Lara Bunte <lara.bu...@yahoo.de> > Subject: [gmx-users] nrexcl in topology > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <1332152362.73030.yahoomail...@web29401.mail.ird.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Hi > > in a topology file in the section [ moleculetypes ] is standing > > ; nrexcl > > 3 > > What do this mean? > > Thanks for help > Greetings > Lara > > > ------------------------------ > > Message: 3 > Date: Mon, 19 Mar 2012 03:26:55 -0700 > From: priya thiyagarajan <priya.thiyagaraja...@gmail.com> > Subject: [gmx-users] extending simulation > To: gmx-users@gromacs.org > Message-ID: > <caeuvtxairnq6ndxppkgg_s34ufzyzvg2z2-bkoaucnqok4f...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello sir,, > > initially i did my simulation for 10ns.. after getting result i analysed it > and thought of extending the simulation for another 10ns.. > > i used following commands.. > > tpbconv *-s md.tpr -o newmd.tpr -extend 10000.00* > > *mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -cpi > state1.cpt -noappend* > > > is it correct.. > > we ll use tpbconv to extend the simulation which terminated in the middle.. > > is it correct to use the same command for completed run... > > please help me with your answer.. > > Thanking you sir, > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/9248f3aa/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 19 Mar 2012 11:27:43 +0100 > From: "R.Perez Garcia" <r.perez.gar...@student.rug.nl> > Subject: Re: [gmx-users] nrexcl in topology > To: Lara Bunte <lara.bu...@yahoo.de>, "gmx-users@gromacs.org" > <gmx-users@gromacs.org> > Message-ID: <7630868d774ff.4f671...@rug.nl> > Content-Type: text/plain; charset="iso-8859-1" > > http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html > > On 19-03-12, Lara Bunte <lara.bu...@yahoo.de> wrote: >> Hi >> >> in a topology file in the section [ moleculetypes ] is standing >> >> ; nrexcl >> >> 3 >> >> What do this mean? >> >> Thanks for help >> Greetings >> Lara >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> 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/Support/Mailing_Lists >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/00e8b769/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 19 Mar 2012 11:43:49 +0100 > From: "lloyd riggs" <lloyd.ri...@gmx.ch> > Subject: Re: [gmx-users] Force constant - Umbrella Sampling > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <20120319104349.106...@gmx.net> > Content-Type: text/plain; charset="utf-8" > > > >From liturature it ranges around 1K for unravling proteins, and > protein-protein dissociations range around 2-3k (kj/mol that is). For small > molecules I have no clue. Id like to know if somone finds out ranges for > any of these though.... > > Stephan Watkins > > -------- Original-Nachricht -------- >> Datum: Mon, 19 Mar 2012 08:48:15 +0000 >> Von: Steven Neumann <s.neuman...@gmail.com> >> An: Discussion list for GROMACS users <gmx-users@gromacs.org>, >> jalem...@vt.edu >> Betreff: [gmx-users] Force constant - Umbrella Sampling > >> Dear Gmx Users, Dear Justin, >> >> As I saw in your tutorial you used the force of 1000 kJ/mol nm2 for the >> harmonic potential. You pulled the whole chain which is quite heavy. Would >> you decrease the force constant for a small molecule (app. 500 Da) during >> the umbrella sampling (e.g. 500 kJ/mol nm2) ? Is it a guess or I should >> check calculations for e.g. 3 force constants and see the influence on the >> final binding free energy? >> >> Thank you, >> >> Steven > > -- > NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! > > Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 95, Issue 125 > ****************************************** > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > 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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists
