Re: [gmx-users] forcefield error for atoms
Thanks Justin! my system is a CNT but I need to insert some atoms in it with no bonds. The best way I found is to make a .pdb and .gro files of the newly constructed system and then without the use of g_x2top command, I added anything needed to the .top file which was made previously without the inserted atoms for the pure CNT system. changes in the .n2t file were also considered including atom introduction. It worked! Cheers On Thu, Mar 26, 2015 at 1:34 PM, mah maz wrote: > Hi Justin, > Thank you! I checked the coordinates and I think there's nothing wrong > with them. The problem might be from the .n2t file. I have some atoms > without any bonds to other atoms in my system. So, in the .n2t file I > assign 0 for bonds to other atoms. And it again stops with the same error > while making the topology file. How can I get rid of this error? > Cheers! > > On Tue, Mar 24, 2015 at 9:00 PM, mah maz wrote: > >> Hi Justin, >> Thanks for your reply. As you guessed correctly, for making a topology >> file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". >> I have a CNT system and I thought I should use g_x2top instead of >> pdb2gmx command. If I'm right, what may cause this error and what would be >> the solution? >> Thanks! >> >> On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: >> >>> Dear all, >>> I need to insert some atoms (without any bonds to other atoms) or even >>> ions in my system. I have created the .pdb, and .gro files, but when I >>> try to generate the .top file it stops with the following error: " >>> forcefield not found for atoms with 0 bonds". Is there a way to solve this >>> problem? >>> Thanks! >>> >> >> > -- 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] forcefield error for atoms
On 3/26/15 5:04 AM, mah maz wrote: Hi Justin, Thank you! I checked the coordinates and I think there's nothing wrong with them. The problem might be from the .n2t file. I have some atoms without any bonds to other atoms in my system. So, in the .n2t file I assign 0 for bonds to other atoms. And it again stops with the same error while making the topology file. How can I get rid of this error? You shouldn't be specifying anything with zero bonds in a CNT system. That makes no sense. You'll have to provide explicit detail of everything you're doing, including the contents of the .n2t file. For a normal CNT, you only need one line, as there are only C atoms and they should all be equally spaced. -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] forcefield error for atoms
Hi Justin, Thank you! I checked the coordinates and I think there's nothing wrong with them. The problem might be from the .n2t file. I have some atoms without any bonds to other atoms in my system. So, in the .n2t file I assign 0 for bonds to other atoms. And it again stops with the same error while making the topology file. How can I get rid of this error? Cheers! On Tue, Mar 24, 2015 at 9:00 PM, mah maz wrote: > Hi Justin, > Thanks for your reply. As you guessed correctly, for making a topology > file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I > have a CNT system and I thought I should use g_x2top instead of pdb2gmx > command. If I'm right, what may cause this error and what would be the > solution? > Thanks! > > On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: > >> Dear all, >> I need to insert some atoms (without any bonds to other atoms) or even >> ions in my system. I have created the .pdb, and .gro files, but when I >> try to generate the .top file it stops with the following error: " >> forcefield not found for atoms with 0 bonds". Is there a way to solve this >> problem? >> Thanks! >> > > -- 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] forcefield error for atoms
On 3/24/15 10:30 AM, mah maz wrote: Hi Justin, Thanks for your reply. As you guessed correctly, for making a topology file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I have a CNT system and I thought I should use g_x2top instead of pdb2gmx command. If I'm right, what may cause this error and what would be the solution? Either the input coordinates are not suitable for constructing the topology, or the .n2t file is constructed incorrectly. The fact that g_x2top found atoms with zero bonds indicates that some atoms are outside all possible distance criteria, hence zero bonds. -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] forcefield error for atoms
Hi Justin, Thanks for your reply. As you guessed correctly, for making a topology file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I have a CNT system and I thought I should use g_x2top instead of pdb2gmx command. If I'm right, what may cause this error and what would be the solution? Thanks! On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: > Dear all, > I need to insert some atoms (without any bonds to other atoms) or even > ions in my system. I have created the .pdb, and .gro files, but when I > try to generate the .top file it stops with the following error: " > forcefield not found for atoms with 0 bonds". Is there a way to solve this > problem? > Thanks! > -- 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] forcefield error for atoms
On 3/22/15 2:11 PM, mah maz wrote: Dear all, I need to insert some atoms (without any bonds to other atoms) or even ions in my system. I have created the .pdb, and .gro files, but when I try to generate the .top file it stops with the following error: " forcefield not found for atoms with 0 bonds". Is there a way to solve this problem? Thanks! You'll need to provide exact commands. This looks like a g_x2top error, but it doesn't make sense why you would be using it in this case. -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.
