Re: [gmx-users] KALP-15 in DPPC tutorial
On 3/16/15 12:08 AM, BAOLIN HUANG wrote: Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I You should never, at any point, have 888444 atoms in the system. Likely you've added water to the inflated system. Don't. got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? You start with 128, InflateGRO prints out how many it removes...then use a text editor. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] KALP-15 in DPPC tutorial
check your popc128.top or topol.top file ; Include POPC chain topology #include popc.itp and ; Include water topology #include gromos53a6_lipid.ff/spc.itp and always update the no of atoms in you .gro file On Mon, Mar 16, 2015 at 10:31 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: firstly go back to check your system.gro file which you made bu cat DPPC.gro new_box.gro system.gro remove some line between the merging of two file update the no of atoms then do your next step On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG baolin.hu...@qut.edu.au wrote: Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? Kind regards, Alex Huang -- 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] KALP-15 in DPPC tutorial
firstly go back to check your system.gro file which you made bu cat DPPC.gro new_box.gro system.gro remove some line between the merging of two file update the no of atoms then do your next step On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG baolin.hu...@qut.edu.au wrote: Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? Kind regards, Alex Huang -- 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] KALP-15 in DPPC tutorial
Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? Kind regards, Alex Huang -- 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.
