[gmx-users] minimization is not converging (Bratin Kumar Das)
>> getting failed for my system Not clear to me. What are the errors? Did you passed all the steps. CHARMM-ui is quite robust. So if the initial structure of the protein and the pdb correctly formated and complete, CHARMM-GUI should work. Stéphane - Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > > St?phane > > -- > > Message: 5 > Date: Thu, 6 Sep 2018 19:55:07 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] minimization is not converging > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you sir > > On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > > > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > > Respected Dr. Justin > > > To avoid the complicacy I > solvated > > > only the protein pdb in a pbc box and tried for minimizatin. There also > > > minimization is not converging. Sir, till now I learned to carry out > > > protein ligand system md simulation successfully. I tried all possible > > ways > > > to simulate the my membrane protein system. I failed. Is it possible > that > > > the PDB file itself have some serious issue with its coordinates. the > > > structure refinement is required may be. > > > > It may, and I have already suggested a few things for you to check. > > Please do so. > > > > If you can provide more specific diagnostics of what is happening, > > someone on this list might be able to suggest something. What you've > > provided thus far is a generic instability that no one can diagnose. > > Investigate the structure, check for pdb2gmx warnings, follow the > > diagnostics I've already suggested, and report back with specific > > observations, a PDB code, and exact errors or warnings you get from any > > program if you need further help. > > > > -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.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. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 > ** > -- > 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: Thu, 6 Sep 2018 22:42:01 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: Re: [gmx-users] minimization is not converging (Bratin Kumar Das) Message-ID: Content-Type: text/plain; charset="UTF-8" Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wro
Re: [gmx-users] minimization is not converging (Bratin Kumar Das)
Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > > Stéphane > > -- > > Message: 5 > Date: Thu, 6 Sep 2018 19:55:07 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] minimization is not converging > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Thank you sir > > On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > > > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > > Respected Dr. Justin > > > To avoid the complicacy I > solvated > > > only the protein pdb in a pbc box and tried for minimizatin. There also > > > minimization is not converging. Sir, till now I learned to carry out > > > protein ligand system md simulation successfully. I tried all possible > > ways > > > to simulate the my membrane protein system. I failed. Is it possible > that > > > the PDB file itself have some serious issue with its coordinates. the > > > structure refinement is required may be. > > > > It may, and I have already suggested a few things for you to check. > > Please do so. > > > > If you can provide more specific diagnostics of what is happening, > > someone on this list might be able to suggest something. What you've > > provided thus far is a generic instability that no one can diagnose. > > Investigate the structure, check for pdb2gmx warnings, follow the > > diagnostics I've already suggested, and report back with specific > > observations, a PDB code, and exact errors or warnings you get from any > > program if you need further help. > > > > -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.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. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 > ** > -- > 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] minimization is not converging (Bratin Kumar Das)
Hi Did you try to use CHARMM-gui and use the gromacs files generated for this system to see if your problem is resolved? Stéphane -- Message: 5 Date: Thu, 6 Sep 2018 19:55:07 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] minimization is not converging Message-ID: Content-Type: text/plain; charset="UTF-8" Thank you sir On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > Respected Dr. Justin > > To avoid the complicacy I solvated > > only the protein pdb in a pbc box and tried for minimizatin. There also > > minimization is not converging. Sir, till now I learned to carry out > > protein ligand system md simulation successfully. I tried all possible > ways > > to simulate the my membrane protein system. I failed. Is it possible that > > the PDB file itself have some serious issue with its coordinates. the > > structure refinement is required may be. > > It may, and I have already suggested a few things for you to check. > Please do so. > > If you can provide more specific diagnostics of what is happening, > someone on this list might be able to suggest something. What you've > provided thus far is a generic instability that no one can diagnose. > Investigate the structure, check for pdb2gmx warnings, follow the > diagnostics I've already suggested, and report back with specific > observations, a PDB code, and exact errors or warnings you get from any > program if you need further help. > > -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.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. End of gromacs.org_gmx-users Digest, Vol 173, Issue 17 ** -- 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.
