Re: [gmx-users] No default U-B types charmm
Hi Justin and Mark You can hack the topology to fix it, but the best bet is to strip waters, process with pdb2gmx to get a topology for everything that's not water, then add back the water coordinates from the original coordinate file and adjust [molecules] accordingly It worked Thanks. So in brief it goes like this: 1) build membrane with CHARMMgui 2) Remove ions and water from CHARMMGUI pdb and save just the membrane pdb. Use this pdb with pdb2gmx to get top file (I used charmm36) 3) Modify [molecules] in top file (add ions and waters information manually) JIom On Mon, Mar 3, 2014 at 9:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 3:56 PM, gromacs query wrote: What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be there. I am following Justin's suggestion to remove moleculetype from top file (still not solved and trying, will let you know; I am newbie to gromacs) Hopefully you're not removing entire [moleculetype] directives, that would be rather horrible. The proper solution is to not process waters with pdb2gmx. You can hack the topology to fix it, but the best bet is to strip waters, process with pdb2gmx to get a topology for everything that's not water, then add back the water coordinates from the original coordinate file and adjust [molecules] accordingly. If you are very new to Gromacs, invest some time working with tutorials simple systems to familiarize yourself with the format before doing these manipulations. In the long run, it will save you time and mistakes. -Justin thanks On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Mar 3, 2014 at 7:25 PM, gromacs query gromacsqu...@gmail.com wrote: Hi Justin Its problem with the waters I think. Can't be, they have no U-B. I found conflict in water atom names: charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2OT -0.834 0 H1HT0.417 1 H2HT0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 10:57 AM, gromacs query wrote: Hi All I am trying to use charmm36 (charmm36-jan2014 from charmm website) with popc membrane built using charmm-gui (have water and ions). I used commands as follows: pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014 editconf -f popc.gro -o popc_box.gro -c -d 0.0 grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr I get this error: (so many) ERROR 11520 [file topol.top, line 184419]: No default U-B types What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? Mark Where are UB for charmm36? This shouldn't happen. Can you please identify what atoms are causing the failure? It may help to simplify by working only with a single lipid rather than a full membrane. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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] No default U-B types charmm
On Mon, Mar 3, 2014 at 7:25 PM, gromacs query gromacsqu...@gmail.comwrote: Hi Justin Its problem with the waters I think. Can't be, they have no U-B. I found conflict in water atom names: charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2OT -0.834 0 H1HT0.417 1 H2HT0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 10:57 AM, gromacs query wrote: Hi All I am trying to use charmm36 (charmm36-jan2014 from charmm website) with popc membrane built using charmm-gui (have water and ions). I used commands as follows: pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014 editconf -f popc.gro -o popc_box.gro -c -d 0.0 grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr I get this error: (so many) ERROR 11520 [file topol.top, line 184419]: No default U-B types What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? Mark Where are UB for charmm36? This shouldn't happen. Can you please identify what atoms are causing the failure? It may help to simplify by working only with a single lipid rather than a full membrane. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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] No default U-B types charmm
What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be there. I am following Justin's suggestion to remove moleculetype from top file (still not solved and trying, will let you know; I am newbie to gromacs) thanks On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Mar 3, 2014 at 7:25 PM, gromacs query gromacsqu...@gmail.com wrote: Hi Justin Its problem with the waters I think. Can't be, they have no U-B. I found conflict in water atom names: charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2OT -0.834 0 H1HT0.417 1 H2HT0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 10:57 AM, gromacs query wrote: Hi All I am trying to use charmm36 (charmm36-jan2014 from charmm website) with popc membrane built using charmm-gui (have water and ions). I used commands as follows: pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014 editconf -f popc.gro -o popc_box.gro -c -d 0.0 grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr I get this error: (so many) ERROR 11520 [file topol.top, line 184419]: No default U-B types What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? Mark Where are UB for charmm36? This shouldn't happen. Can you please identify what atoms are causing the failure? It may help to simplify by working only with a single lipid rather than a full membrane. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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. -- 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.
