Re: [gmx-users] OPLS-AA Unknown Atomtype
Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? Thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 23, 2011 2:07 PM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond_atomtype CA1 --- ~~ I understand that I have not inserted CA1 into atomtypes.atp. because if I add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it. The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx. What you are trying to avoid is what you have to do - if you introduce a new atom type and intend to use it in any bonded interactions, you must introduce relevant parameters for all the interactions in which it will participate. So I denoted the type of it as a known carbon atom in my topology file (in the attachment). I thought in OPLS-AA, CA1 can cite this known atom since CA1 is just a name. Names and types are different. You can name an atom anything you like, but atom types must be judiciously assigned. Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give bonds, angles, and dihedrals of CA1. If you have inserted all of the correct parameters in these files, you would not receive the error above. Perhaps herein lies the problem - if you have modified ffnonbonded.itp (which belongs to the force field organization of the 4.5.x series), it will have no effect on a 4.0.7 executable, which is being called above. So (at least) one of two possibilities is true: 1. You're not using the Gromacs version you intend to. 2. You haven't introduced all of the parameters you need to. The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I know, but that's how
Re: [gmx-users] OPLS-AA Unknown Atomtype
Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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] OPLS-AA Unknown Atomtype
HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need to modify. Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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-- 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] OPLS-AA Unknown Atomtype
Yao Yao wrote: HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the The net charge problem cannot be solved by adding ions. A fractional charge of that magnitude indicates the charges in the topology are wrong. angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need to modify. The only file that contains [bondtypes], [angletypes], etc is ffoplsaabon.itp, so if the entries are indeed there, have the correct format, and are placed appropriately, you wouldn't be getting this error. So unless you post the exact lines in their exact context, I'm left to assume that you've done something else wrong. -Justin Thanks, yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, August 29, 2011 3:41 AM *Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] OPLS-AA Unknown Atomtype
Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error Unknown Molecule_Atomtype. I have opened all the files in the OPLS force field but really do not see any other files I could modify. Does anyone have this kind of problem before? Thanks, Yao -- 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] OPLS-AA Unknown Atomtype
Yao Yao wrote: Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error Unknown Molecule_Atomtype. I have opened all the files in the OPLS force field but really do not see any other files I could modify. Please copy and paste the exact error message from the terminal, as well as the command that gave the error. I can't find any reference in the code to the error you posted, but the actual screen output will have all the relevant information. -Justin Does anyone have this kind of problem before? Thanks, Yao -- 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] OPLS-AA Unknown Atomtype
Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond_atomtype CA1 --- ~~ I understand that I have not inserted CA1 into atomtypes.atp. because if I add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it. The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx. What you are trying to avoid is what you have to do - if you introduce a new atom type and intend to use it in any bonded interactions, you must introduce relevant parameters for all the interactions in which it will participate. So I denoted the type of it as a known carbon atom in my topology file (in the attachment). I thought in OPLS-AA, CA1 can cite this known atom since CA1 is just a name. Names and types are different. You can name an atom anything you like, but atom types must be judiciously assigned. Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give bonds, angles, and dihedrals of CA1. If you have inserted all of the correct parameters in these files, you would not receive the error above. Perhaps herein lies the problem - if you have modified ffnonbonded.itp (which belongs to the force field organization of the 4.5.x series), it will have no effect on a 4.0.7 executable, which is being called above. So (at least) one of two possibilities is true: 1. You're not using the Gromacs version you intend to. 2. You haven't introduced all of the parameters you need to. The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I know, but that's how it works). So for the problematic atom (type opls_137) the bond_atomtype is CT (second column of ffnonbonded.itp in [atomtypes]). So generally speaking, I am wondering if an atom with a different name gets introduced into OPLS, it has to be denoted again (bonds, angles, ...) and added into the atomtypes.atp, even it is a carbon atom? And do you happen to know any tutorial about how to introduce new molecules into OPLS? Again, names are irrelevant but types are critical. There is no tutorial, per se, but the instructions are on the wiki in a general form: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Most of the instructions are designed around residues for which pdb2gmx will act. In your case, any new atom types need to be defined in ffnonbonded.itp and then bonded interactions making use of those types in ffbonded.itp. -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
