[gmx-users] About -chainsep and -ter
於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到: Hi everyone, My pdb file is consist of two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . The -ter option allows you to change the protonation state of the termini. The shorthand iso means instead of, implying that charged termini are the default. If you do not need to alter the protonation state of the termini, then you do not need the -ter option. Thanks for the explain. Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. Your system exploded because pdb2gmx likely tried to make your two chains one continuous protein, forming an unrealistic bond between the C-terminal of chain A and the N-terminal of chain B. By removing the TER delimiter, you've essentially told pdb2gmx that you have one protein, not two. If I don't use -chainsep ter, then pdb2gmx will consider two chains as Protein-A and Protein-B. The inter-disulfide bonds between two-chains will be lost. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. Assuming that the y response indicates that you want separate chains, that's why this approach works. Regardless, if you have two distinct proteins (i.e. the backbones are not continuous), you do not want the chains to be considered continuous. Disulfides are created in a separate mechanism utilizing specbond.dat and is independent of the use of -chainsep. The question is , Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with chain starting with residue PHE1 (chain id 'B', atom 165 N)? [n/y] Then I choose y, I think it's the same as -chainsep ter. Isn' it? But for -chainsep ter, there is errors in mdrun. For -chainsep interactive and type y, everything correct. They seems to the same in my two chain system. There is likely some difference (probably a single bond) that is causing the problem. -- 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] About -chainsep and -ter
Hsin-Lin Chiang wrote: 於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到: Hi everyone, My pdb file is consist of two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . The -ter option allows you to change the protonation state of the termini. The shorthand iso means instead of, implying that charged termini are the default. If you do not need to alter the protonation state of the termini, then you do not need the -ter option. Thanks for the explain. Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. Your system exploded because pdb2gmx likely tried to make your two chains one continuous protein, forming an unrealistic bond between the C-terminal of chain A and the N-terminal of chain B. By removing the TER delimiter, you've essentially told pdb2gmx that you have one protein, not two. If I don't use -chainsep ter, then pdb2gmx will consider two chains as Protein-A and Protein-B. The inter-disulfide bonds between two-chains will be lost. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. Assuming that the y response indicates that you want separate chains, that's why this approach works. Regardless, if you have two distinct proteins (i.e. the backbones are not continuous), you do not want the chains to be considered continuous. Disulfides are created in a separate mechanism utilizing specbond.dat and is independent of the use of -chainsep. The question is , Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with chain starting with residue PHE1 (chain id 'B', atom 165 N)? [n/y] Then I choose y, I think it's the same as -chainsep ter. Isn' it? But for -chainsep ter, there is errors in mdrun. For -chainsep interactive and type y, everything correct. Please post a diff of the two topologies (the one that failed and the one that worked). -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] About -chainsep and -ter
Please post a diff of the two topologies (the one that failed and the one that worked). -Justin I use diff bash commend on the two top file and save to log file. The different was long but they both have three inter-disulfide bond There are 3973 lines in different log file.#160; I'm not sure if I can post all here. Do we have another way to discuss? Sincerely yours, Hsin-Lin -- 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] About -chainsep and -ter
Hsin-Lin Chiang wrote: ** Please post a diff of the two topologies (the one that failed and the one that worked). -Justin I use diff bash commend on the two top file and save to log file. The different was long but they both have three inter-disulfide bond There are 3973 lines in different log file. I'm not sure if I can post all here. Do we have another way to discuss? If you send me your two topologies (off-list), I will take a look at them to see if I can figure out what happened. -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] About -chainsep and -ter
I suspect this is a bug, so I have filed an issue on redmine: http://redmine.gromacs.org/issues/784 In a previous issue (http://redmine.gromacs.org/issues/544), the -chainsep interactive option did not work, but now it does. Conversely, -chainsep ter (which should also work in this case) does not. -Justin Hsin-Lin Chiang wrote: ** Please post a diff of the two topologies (the one that failed and the one that worked). -Justin I use diff bash commend on the two top file and save to log file. The different was long but they both have three inter-disulfide bond There are 3973 lines in different log file. I'm not sure if I can post all here. Do we have another way to discuss? Sincerely yours, Hsin-Lin -- 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] About -chainsep and -ter
I suspect this is a bug, so I have filed an issue on redmine: http://redmine.gromacs.org/issues/784 In a previous issue (http://redmine.gromacs.org/issues/544), the -chainsep interactive option did not work, but now it does. Conversely, -chainsep ter (which should also work in this case) does not. -Justin I get success in pdb2gmx, but I not only delete ter line but also all OXT lines according to this mailing list, http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html But I'm failed when I used mdrun in -chainsep ter case. Hsin-Lin -- 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] About -chainsep and -ter
Hsin-Lin Chiang wrote: I suspect this is a bug, so I have filed an issue on redmine: http://redmine.gromacs.org/issues/784 In a previous issue (http://redmine.gromacs.org/issues/544), the -chainsep interactive option did not work, but now it does. Conversely, -chainsep ter (which should also work in this case) does not. -Justin I get success in pdb2gmx, but I not only delete ter line but also all OXT lines according to this mailing list, http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html But I'm failed when I used mdrun in -chainsep ter case. Right. Even if you somehow force pdb2gmx to write a topology in this case, the bonds are not correct and the termini are incomplete. That will hopefully be resolved when the bug is fixed. For now, you have a workaround. Just use -chainsep interactive and you will get a proper topology. -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] About -chainsep and -ter
Right. Even if you somehow force pdb2gmx to write a topology in this case, the bonds are not correct and the termini are incomplete. That will hopefully be resolved when the bug is fixed. For now, you have a workaround. Just use -chainsep interactive and you will get a proper topology. -Justin I understand now. Thank you very much for your help. Sincerely yours, Hsin-Lin -- 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] About -chainsep and -ter
Hi everyone, My pdb file is consist of#160; two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive#160; and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. They seems to the same in my two chain system. Sincerely yours, Hsin-Lin - starting mdrun 'Protein in water' 750 steps,#160; 15000.0 ps. Warning: 1-4 interaction between 196 and 207 at distance 3.231 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 0, time 0 (ps)#160; LINCS WARNING relative constraint deviation after LINCS: rms 66.078426, max 708.612183 (between atoms 207 and 208) bonds that rotated more than 30 degrees: #160;atom 1 atom 2#160; angle#160; previous, current, constraint length #160;#160;#160; 207#160;#160;#160; 208#160;#160; 90.0#160;#160;#160; 0.1000#160; 70.9612#160;#160;#160;#160;#160; 0.1000 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4# Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps)#160; LINCS WARNING relative constraint deviation after LINCS: rms 67071649.681650, max 719263296.00 (between atoms 207 and 208) bonds that rotated more than 30 degrees: #160;atom 1 atom 2#160; angle#160; previous, current, constraint length #160;#160;#160; 207#160;#160;#160; 208#160;#160; 90.0#160;#160; 70.9612 71926328.#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 212#160;#160;#160; 213#160;#160; 90.0#160;#160;#160; 0.1090#160;#160; 0.1308#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 216#160;#160;#160; 217#160;#160; 40.3#160;#160;#160; 0.1090#160;#160; 0.1090#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 218#160;#160;#160; 219#160;#160; 90.0#160;#160;#160; 0.1090#160;#160; 0.1545#160;#160;#160;#160;#160; 0.1090 #160;#160;#160; 224#160;#160;#160; 225#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3996#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 232#160;#160;#160; 233#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3867#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 238#160;#160;#160; 239#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.1782#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 238#160;#160;#160; 240#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 1.0652#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 243#160;#160;#160; 244#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3092#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 250#160;#160;#160; 251#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.3082#160;#160;#160;#160;#160; 0.1000 #160;#160;#160; 250#160;#160;#160; 252#160;#160; 90.0#160;#160;#160; 0.1000#160;#160; 0.2102#160;#160;#160;#160;#160; 0.1000 step 1: Water molecule starting at atom 10744 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4# Wrote pdb files with previous and current coordinates Segmentation fault #160; -- 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] About -chainsep and -ter
Hsin-Lin Chiang wrote: Hi everyone, My pdb file is consist of two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't understand the meaning of interective termini selection, iso charged . The -ter option allows you to change the protonation state of the termini. The shorthand iso means instead of, implying that charged termini are the default. If you do not need to alter the protonation state of the termini, then you do not need the -ter option. Anyway, I met problem after editconf, genbox, grompp, genion, and grompp. When I execute mdrun, I got the warning and terminated. Please see the long message below my name. Your system exploded because pdb2gmx likely tried to make your two chains one continuous protein, forming an unrealistic bond between the C-terminal of chain A and the N-terminal of chain B. By removing the TER delimiter, you've essentially told pdb2gmx that you have one protein, not two. However, if I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. Assuming that the y response indicates that you want separate chains, that's why this approach works. Regardless, if you have two distinct proteins (i.e. the backbones are not continuous), you do not want the chains to be considered continuous. Disulfides are created in a separate mechanism utilizing specbond.dat and is independent of the use of -chainsep. They seems to the same in my two chain system. There is likely some difference (probably a single bond) that is causing the problem. -Justin Sincerely yours, Hsin-Lin - starting mdrun 'Protein in water' 750 steps, 15000.0 ps. Warning: 1-4 interaction between 196 and 207 at distance 3.231 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 66.078426, max 708.612183 (between atoms 207 and 208) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 207208 90.00.1000 70.9612 0.1000 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.4# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4# Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 67071649.681650, max 719263296.00 (between atoms 207 and 208) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 207208 90.0 70.9612 71926328. 0.1000 212213 90.00.1090 0.1308 0.1090 216217 40.30.1090 0.1090 0.1090 218219 90.00.1090 0.1545 0.1090 224225 90.00.1000 0.3996 0.1000 232233 90.00.1000 0.3867 0.1000 238239 90.00.1000 0.1782 0.1000 238240 90.00.1000 1.0652 0.1000 243244 90.00.1000 0.3092 0.1000 250251 90.00.1000 0.3082 0.1000 250252 90.00.1000 0.2102 0.1000 step 1: Water molecule starting at atom 10744 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4# Wrote pdb files with previous and current coordinates Segmentation fault -- 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
