RE: [gmx-users] error with x2top.
Yep You are right. I will try my best to change the files accordingly. Thanks > Date: Tue, 25 Sep 2012 17:05:20 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with x2top. > > > > On 9/25/12 5:02 PM, Elie M wrote: > > > > Thanks for your reply. I guess either way (x2top or pdb2gmx), I have > > problems. pdb2gmx is giving the same old error residue 'UNK' is not found > > in topology residue file whereas strangely enough x2top did not complain > > and was able to assign topologies for 73 atoms out of 94 so maybe it is > > easier to use x2top because in the other case I have to change files and I > > have no experience in this whatsoever and I am really tight on time. What > > do you personally think? > > > > Neither tool is guaranteed to produce a topology for an arbitrary molecule. > If > g_x2top does not have the right parameters, it will fail. If pdb2gmx does > not > have the right parameters, it will fail. g_x2top further assumes that some > generic set of atom types and functional groups will address whatever it is > that > you're working with. Sometimes that's appropriate, sometimes it's not. > Either > way, you're going to have to modify either the .n2t file or the .rtp file for > your chosen force field. Regardless of the route you choose, you're going to > have to come up with parameters for your molecule and learn how these files > work > so you can modify them. Parameterization is an expert topic for a reason. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] error with x2top.
On 9/25/12 5:02 PM, Elie M wrote: Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Neither tool is guaranteed to produce a topology for an arbitrary molecule. If g_x2top does not have the right parameters, it will fail. If pdb2gmx does not have the right parameters, it will fail. g_x2top further assumes that some generic set of atom types and functional groups will address whatever it is that you're working with. Sometimes that's appropriate, sometimes it's not. Either way, you're going to have to modify either the .n2t file or the .rtp file for your chosen force field. Regardless of the route you choose, you're going to have to come up with parameters for your molecule and learn how these files work so you can modify them. Parameterization is an expert topic for a reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
RE: [gmx-users] error with x2top.
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Regards > Date: Tue, 25 Sep 2012 16:32:33 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with x2top. > > > > On 9/25/12 4:28 PM, Elie M wrote: > > > > Dear all, > > i am trying to convert a .gro file into a top file using .x2top but not all > > atoms can be assigned forcefields and the code stops with the error: > > Generating bonds from distances...atom 94Can not find forcefield for atom > > C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not > > find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom > > C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not > > find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom > > C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not > > find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom > > O-18 withFatal error:Could only find a forcefield type for > > 73 out of 94 atoms > > I looked at the .atp and n2t files. I am not sure where to start. is the > > second column partial charges? how to determine these? are they > > automatically determined ..what about the numbers at the end after each > > atom symbol? Is there any clear examples of how to do this? Any help would > > be appreciated. Thanks > > > > The format is explained in full here: > > http://www.gromacs.org/Documentation/File_Formats/.n2t_File > > The charges and atom types are determined by parameterizing the molecule of > interest, but if you're going to do that much work, it's probably simpler to > create an .rtp entry and have pdb2gmx do the work. g_x2top is usually > intended > to create simple topologies for simple molecules. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] error with x2top.
On 9/25/12 4:28 PM, Elie M wrote: Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks The format is explained in full here: http://www.gromacs.org/Documentation/File_Formats/.n2t_File The charges and atom types are determined by parameterizing the molecule of interest, but if you're going to do that much work, it's probably simpler to create an .rtp entry and have pdb2gmx do the work. g_x2top is usually intended to create simple topologies for simple molecules. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] error with x2top.
Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks Elie -- gmx-users mailing listgmx-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
