Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote: Hi Justin, No. I have not added any ions. Well, then it's a complete mystery. You'll have to go through your coordinate file and topology and count the relevant number of molecules or atoms and decide for yourself where the mismatch comes from. Nothing that you've provided explains where the problem comes from. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] mismatch in coordinate and topology
Hi Justin, No. I have not added any ions. Samrat From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, October 21, 2011 11:39 AM Subject: Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: > Hi Justin, > (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has >54 atoms. The error msg. does not show any specific mismatching. > (2) I forgot to mention that I have increased the number of the atoms on the >top (2nd line) of the gro file after adding the 2 ligands. > Did you add any ions after solvation? And if so, did you update your topology? If SOL is the last entry, then likely not. -Justin > Samrat > *From:* Justin A. Lemkul > *To:* Samrat Pal ; Discussion list for GROMACS users > > *Sent:* Friday, October 21, 2011 8:49 AM > *Subject:* Re: [gmx-users] mismatch in coordinate and topology > > > > Samrat Pal wrote: > > Hi All, > > I am trying to minimize the chryptochrome structure that has one >FAD and one MHF ligand bound to it. > > Following are the steps that I performed > > (1) Created the protein coordinate(gro) file using pdb2gmx command and >choosing GROMOS43a1 force-field > > (2) Created the FAD and MHF topology and coordinate files using PRODRG >where I have chosen > > a) no chirality, b) full charge and (c) no minimization. /I have not seen >any option for choosing force-field in the server/. (3) I have taken the >corresponding coordinate and topology files from that server, appended the >coordinates of both the ligands in the gro file of the protein (before the box >vector i.e. the last line), and also included the ligand topology files in the >topol.top file after "posre.itp" and before "spc.itp"accordingly. > > Regarding (2) and (3) - the output of the PRODRG server will likely give poor > results. See the paper linked from > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. > > > (4) I have also added two lines in the [molecules] section like, > > FAD 1 > > MHF 1 > > (5) Then I have created a cubic box where I have taken the coordinate and >solvated the protein+ligands coordinate with spc water model using genbox. > > > A dodecahedral box is likely going to be more efficient, but this is not > relevant to the problem at hand. > > > (6) Then I tried to create the em.tpr file from em.mdp file using grompp >command. > > I got the following error message --- number of atoms in the coordinate >file does not match with topology file where topology file has 31 missing >atoms according to the numbers shown in the error message. > > > OK, so do any of your molecules consist of 31 atoms? Do you get any notes > about non-matching names? > > > I have checked the topology file after solvation and it is updated having >the last line of the file with SOL 34741. > > I have been using gromacs for few months and I have successfully >simulated systems with ligands before. Could anybody please tell me where I am >doing wrong? > Did you properly increment the number of atoms in the coordinate file after > adding your ligands? > > -Justin > > -- > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote: Hi Justin, (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching. (2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands. Did you add any ions after solvation? And if so, did you update your topology? If SOL is the last entry, then likely not. -Justin Samrat *From:* Justin A. Lemkul *To:* Samrat Pal ; Discussion list for GROMACS users *Sent:* Friday, October 21, 2011 8:49 AM *Subject:* Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: > Hi All, > I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. > Following are the steps that I performed > (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field > (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen > a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. > (4) I have also added two lines in the [molecules] section like, > FAD 1 > MHF 1 > (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. > A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. > (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. > I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. > OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? > I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. > I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] mismatch in coordinate and topology
Hi Justin, (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching. (2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands. Samrat From: Justin A. Lemkul To: Samrat Pal ; Discussion list for GROMACS users Sent: Friday, October 21, 2011 8:49 AM Subject: Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: > Hi All, > I am trying to minimize the chryptochrome structure that has one FAD >and one MHF ligand bound to it. > Following are the steps that I performed > (1) Created the protein coordinate(gro) file using pdb2gmx command and >choosing GROMOS43a1 force-field > (2) Created the FAD and MHF topology and coordinate files using PRODRG where >I have chosen > a) no chirality, b) full charge and (c) no minimization. /I have not seen any > option for choosing force-field in the server/. (3) I have taken the > corresponding coordinate and topology files from that server, appended the > coordinates of both the ligands in the gro file of the protein (before the > box vector i.e. the last line), and also included the ligand topology files > in the topol.top file after "posre.itp" and before "spc.itp"accordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. > (4) I have also added two lines in the [molecules] section like, > FAD 1 > MHF 1 > (5) Then I have created a cubic box where I have taken the coordinate and >solvated the protein+ligands coordinate with spc water model using genbox. > A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. > (6) Then I tried to create the em.tpr file from em.mdp file using grompp > command. > I got the following error message --- number of atoms in the coordinate file >does not match with topology file where topology file has 31 missing atoms >according to the numbers shown in the error message. > OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? > I have checked the topology file after solvation and it is updated having the > last line of the file with SOL 34741. > I have been using gromacs for few months and I have successfully simulated >systems with ligands before. Could anybody please tell me where I am doing >wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] mismatch in coordinate and topology
Samrat Pal wrote: Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] mismatch in coordinate and topology
Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. I have not seen any option for choosing force-field in the server. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? thanks in advance Samrat -- 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
