Re: [gmx-users] Grompp error: No default g96angle type
shahid nayeem wrote: HI I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives any eror using ffG43a1. .top file produced shows all bonds (Fe SD of MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error lines does not have bond/angle nomenclature such as 809 810 2gb_30 810 811 2gb_29 810 1068 2 812 813 2gb_4 812 814 2gb_9 814 815 2gb_2 810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp file of force-field and adding these bonds and giving some name to it but got the same error in grompp. Modifying an .rtp entry will do nothing since this bond exists between two (presumably) non-sequential residues. Though .top file shows these bonds the .gro file generated does not show these bonds in VMD while original pdb file shows these bonds. thanking you. VMD's concept of bonds is irrelevant, it's simply guessing where they should be based on interatomic distances. Unfortunately, GROMACS does not work out of the box with heme-containing species, but these types of simulations are in no way novel, so obviously parameters for these missing terms should be available somewhere. Consult the literature, and if necessary, contact the authors of relevant papers - they should be able to reproduce their work, at least, we hope :) -Justin waiting for your suggestion. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. One of the most important choices when conducting MD simulations is the force field. You'll have to find one that works. It appears that (unfortunately) the Gromos force fields do not work out of the box when heme is involved. If you want specific advice about other force fields, you'll have to describe your problem much better than gives error at some point. No one can help you sort that out. You'd do well to look into the literature. Simulations of heme proteins are not novel, so clearly others have made this work, and in some cases, parameters might be provided for the terms that are missing. -Justin shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself
Re: [gmx-users] Grompp error: No default g96angle type
HI I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives any eror using ffG43a1. .top file produced shows all bonds (Fe SD of MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error lines does not have bond/angle nomenclature such as 809 810 2gb_30 810 811 2gb_29 810 1068 2 812 813 2gb_4 812 814 2gb_9 814 815 2gb_2 810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp file of force-field and adding these bonds and giving some name to it but got the same error in grompp. Though .top file shows these bonds the .gro file generated does not show these bonds in VMD while original pdb file shows these bonds. thanking you. waiting for your suggestion. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. One of the most important choices when conducting MD simulations is the force field. You'll have to find one that works. It appears that (unfortunately) the Gromos force fields do not work out of the box when heme is involved. If you want specific advice about other force fields, you'll have to describe your problem much better than gives error at some point. No one can help you sort that out. You'd do well to look into the literature. Simulations of heme proteins are not novel, so clearly others have made this work, and in some cases, parameters might be provided for the terms that are missing. -Justin shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
[gmx-users] Grompp error: No default g96angle type
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. Thanks in anticipation of help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Grompp error: No default g96angle type
shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- 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/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/mailing_lists/users.php
Re: [gmx-users] Grompp error: No default g96angle type
Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Grompp error: No default g96angle type
shahid nayeem wrote: Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. One of the most important choices when conducting MD simulations is the force field. You'll have to find one that works. It appears that (unfortunately) the Gromos force fields do not work out of the box when heme is involved. If you want specific advice about other force fields, you'll have to describe your problem much better than gives error at some point. No one can help you sort that out. You'd do well to look into the literature. Simulations of heme proteins are not novel, so clearly others have made this work, and in some cases, parameters might be provided for the terms that are missing. -Justin shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+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 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- 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/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/mailing_lists/users.php -- 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
