[gmx-users] disulfide bond, molecule type
No. You said before you had broken chains. Applying trjconv -pbc mol fixes this issue. Molecules can be "broken" across periodic boundaries and is an entirely normal phenomenon. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions >/ And I tried another way. />/ I change the content of .gro file. />/ I plus the number of residues in A-chain to B-chain's residue number. />/ And this new gro file shows the correct snapshot in VMD. />/ for example />/ my a-chain has 21 residues, b-chain has 30 residues. />/ In output .gro file the residue number is 1 to 21 and 1 to 30. />/ />/ I'm afraid VMD got confused for the repeat number 1 to 21. />/ So I change 1-30 in b-chain to 22-51. />/ Then snapshot in VMD become correct. / Then this was primarily VMD's issue. -Justin Thank you for your help. I think I have no problem now. 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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: >/ />>/ I doubt the chain identifiers are relevant. Both .gro and .pdb files should />>/ display properly. The only odd instance I can think of is that without separate />>/ chains, some programs may interpret the protein coordinates as a single />>/ molecule, but I would think that would only happen in the rarest of cases (when />>/ the termini are so close that the heuristic bond search algorithms think there />>/ should be a bond between the chains). />>/ />>/ When invoking trjconv, did you use any option to modify the periodic representation? />/ I used />/ trjconv -pbc mol -center -n index.ndx .. / OK, so this was just a periodicity issue all along. I'm sorry that I don't understand. So I did something wrong in PBC by trjconv? No. You said before you had broken chains. Applying trjconv -pbc mol fixes this issue. Molecules can be "broken" across periodic boundaries and is an entirely normal phenomenon. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I tried another way. I change the content of .gro file. I plus the number of residues in A-chain to B-chain's residue number. And this new gro file shows the correct snapshot in VMD. for example my a-chain has 21 residues, b-chain has 30 residues. In output .gro file the residue number is 1 to 21 and 1 to 30. I'm afraid VMD got confused for the repeat number 1 to 21. So I change 1-30 in b-chain to 22-51. Then snapshot in VMD become correct. Then this was primarily VMD's issue. -Justin >/ Here I chose a-chain for center and protein for output. />>/ >/ Do I have any commend can use instead of chain identifier A and B />>/ />/ mannually? />>/ />/ />>/ / />>/ I don't understand your question here. />/ I'm sorry. />/ I separate chains manually. />/ (Add chain identifier A and B manually in vim) />/ Do I have any commend of GROMACS can handle this and I don't need to />/ separate chains manually. />/ / With a merged chain, I think you will always have to add them back in. Thank you. -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] disulfide bond, molecule type
>/ />>/ I doubt the chain identifiers are relevant. Both .gro and .pdb files should />>/ display properly. The only odd instance I can think of is that without separate />>/ chains, some programs may interpret the protein coordinates as a single />>/ molecule, but I would think that would only happen in the rarest of cases (when />>/ the termini are so close that the heuristic bond search algorithms think there />>/ should be a bond between the chains). />>/ />>/ When invoking trjconv, did you use any option to modify the periodic representation? />/ I used />/ trjconv -pbc mol -center -n index.ndx .. / OK, so this was just a periodicity issue all along. I'm sorry that I don't understand. So I did something wrong in PBC by trjconv? And I tried another way. I change the content of .gro file. I plus the number of residues in A-chain to B-chain's residue number. And this new gro file shows the correct snapshot in VMD. for example my a-chain has 21 residues, b-chain has 30 residues. In output .gro file the residue number is 1 to 21 and 1 to 30. I'm afraid VMD got confused for the repeat number 1 to 21. So I change 1-30 in b-chain to 22-51. Then snapshot in VMD become correct. >/ Here I chose a-chain for center and protein for output. />>/ >/ Do I have any commend can use instead of chain identifier A and B />>/ />/ mannually? />>/ />/ />>/ / />>/ I don't understand your question here. />/ I'm sorry. />/ I separate chains manually. />/ (Add chain identifier A and B manually in vim) />/ Do I have any commend of GROMACS can handle this and I don't need to />/ separate chains manually. />/ / With a merged chain, I think you will always have to add them back in. Thank you. -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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that would only happen in the rarest of cases (when the termini are so close that the heuristic bond search algorithms think there should be a bond between the chains). When invoking trjconv, did you use any option to modify the periodic representation? I used trjconv -pbc mol -center -n index.ndx .. OK, so this was just a periodicity issue all along. Here I chose a-chain for center and protein for output. >/ Do I have any commend can use instead of chain identifier A and B />/ mannually? />/ / I don't understand your question here. I'm sorry. I separate chains manually. (Add chain identifier A and B manually in vim) Do I have any commend of GROMACS can handle this and I don't need to separate chains manually. With a merged chain, I think you will always have to add them back in. -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] disulfide bond, molecule type
I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that would only happen in the rarest of cases (when the termini are so close that the heuristic bond search algorithms think there should be a bond between the chains). When invoking trjconv, did you use any option to modify the periodic representation? I used trjconv -pbc mol -center -n index.ndx .. Here I chose a-chain for center and protein for output. >/ Do I have any commend can use instead of chain identifier A and B />/ mannually? />/ / I don't understand your question here. I'm sorry. I separate chains manually. (Add chain identifier A and B manually in vim) Do I have any commend of GROMACS can handle this and I don't need to separate chains manually. Hsin-Lin -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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residues then they probably have infinite coordinates and your simulation has blown up and is therefore junk. -Justin I convert .gro to .pdb by trjconv and add chain identifier A and B to .pdb file. (Because of -chainsep all chain identifier was delete before MD) Then VMD and Pymol shows correct as Rasmol. So, maybe the error of snapshot was just because chain identifiers were lacked before. I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that would only happen in the rarest of cases (when the termini are so close that the heuristic bond search algorithms think there should be a bond between the chains). When invoking trjconv, did you use any option to modify the periodic representation? Do I have any commend can use instead of chain identifier A and B mannually? I don't understand your question here. -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] disulfide bond, molecule type
If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residues then they probably have infinite coordinates and your simulation has blown up and is therefore junk. -Justin I convert .gro to .pdb by trjconv and add chain identifier A and B to .pdb file. (Because of -chainsep all chain identifier was delete before MD) Then VMD and Pymol shows correct as Rasmol. So, maybe the error of snapshot was just because chain identifiers were lacked before. Do I have any commend can use instead of chain identifier A and B mannually? 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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: Hsin-Lin Chiang wrote: >/ Hi, />/ />/ I'm trying to heat a protein. />/ There are two chains, A-chain and B-chain. />/ Two disulfide bonds are between A-chain and B-chain. />/ As I know, I should let A-chain and B-chain belong to the same [molecule />/ type] in .top file if I want to have the two inter-bonds. />/ />/ So, I delete the TER line between A-chain and B-chain in .pdb file. />/ And then I use "pdb2gmx -chainsep interactive" on it . />/ />/ I got the two bonds successfully. />/ But after heating, the length of A-chain and B-chain in VMD was changed. />/ The number of residues in A-chain increase and the ones of B-chain />/ decrease. />/ It means some residues move from B-chain to A-chain. />/ How should I prevent this kind of error happen. />/ / The labeling changes? Is this something VMD is doing or something you can actually demonstrate in the coordinate file? Labeling didn't change. I don't know what VMD did. It seems to some residues disappear, A-chain was elongated, and B-chain was shortened. I also tried Pymol. It gave me several small crash peptides. But I just tried Ramol, everything looks correct. Something wrong in VMD and Pymol may just because A-chain and B-chain curved extremely after heating. But I'm still afraid Is my output structure wrong by GROMACS? If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residues then they probably have infinite coordinates and your simulation has blown up and is therefore junk. -Justin Sincerely yours, Hsin-Lin >/ Besides, I found even though I only have protein_A which consist both of />/ A-chain and B-chain. />/ The number of first residue of B-chain is started from 1 in .gro file. />/ I thought it should be equal to "the number of A-chain's residues plus 1". />/ />/ And it was also strange that the number of first water molecules was />/ equal to "the number of B-chain plus 1" />/ I thought it should be equal to "the number of A-chain's residues plus />/ the number of B-chain's residues plus 1" />/ />/ Is it a bug? />/ / No, it is the expected output. By default, pdb2gmx does not renumber residues consecutively. This feature was introduced some time ago so that output selections could easily be made in multiple chain molecules like this one. If you want residues renumbered consecutively, either post-process the coordinate files with genconf -renumber or start over and use pdb2gmx -renum. Thank you for your explanation. -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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: >/ Hi, />/ />/ I'm trying to heat a protein. />/ There are two chains, A-chain and B-chain. />/ Two disulfide bonds are between A-chain and B-chain. />/ As I know, I should let A-chain and B-chain belong to the same [molecule />/ type] in .top file if I want to have the two inter-bonds. />/ />/ So, I delete the TER line between A-chain and B-chain in .pdb file. />/ And then I use "pdb2gmx -chainsep interactive" on it . />/ />/ I got the two bonds successfully. />/ But after heating, the length of A-chain and B-chain in VMD was changed. />/ The number of residues in A-chain increase and the ones of B-chain />/ decrease. />/ It means some residues move from B-chain to A-chain. />/ How should I prevent this kind of error happen. />/ / The labeling changes? Is this something VMD is doing or something you can actually demonstrate in the coordinate file? Labeling didn't change. I don't know what VMD did. It seems to some residues disappear, A-chain was elongated, and B-chain was shortened. I also tried Pymol. It gave me several small crash peptides. But I just tried Ramol, everything looks correct. Something wrong in VMD and Pymol may just because A-chain and B-chain curved extremely after heating. But I'm still afraid Is my output structure wrong by GROMACS? Sincerely yours, Hsin-Lin >/ Besides, I found even though I only have protein_A which consist both of />/ A-chain and B-chain. />/ The number of first residue of B-chain is started from 1 in .gro file. />/ I thought it should be equal to "the number of A-chain's residues plus 1". />/ />/ And it was also strange that the number of first water molecules was />/ equal to "the number of B-chain plus 1" />/ I thought it should be equal to "the number of A-chain's residues plus />/ the number of B-chain's residues plus 1" />/ />/ Is it a bug? />/ / No, it is the expected output. By default, pdb2gmx does not renumber residues consecutively. This feature was introduced some time ago so that output selections could easily be made in multiple chain molecules like this one. If you want residues renumbered consecutively, either post-process the coordinate files with genconf -renumber or start over and use pdb2gmx -renum. Thank you for your explanation. -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] disulfide bond, molecule type
Hsin-Lin Chiang wrote: Hi, I'm trying to heat a protein. There are two chains, A-chain and B-chain. Two disulfide bonds are between A-chain and B-chain. As I know, I should let A-chain and B-chain belong to the same [molecule type] in .top file if I want to have the two inter-bonds. So, I delete the TER line between A-chain and B-chain in .pdb file. And then I use "pdb2gmx -chainsep interactive" on it . I got the two bonds successfully. But after heating, the length of A-chain and B-chain in VMD was changed. The number of residues in A-chain increase and the ones of B-chain decrease. It means some residues move from B-chain to A-chain. How should I prevent this kind of error happen. The labeling changes? Is this something VMD is doing or something you can actually demonstrate in the coordinate file? Besides, I found even though I only have protein_A which consist both of A-chain and B-chain. The number of first residue of B-chain is started from 1 in .gro file. I thought it should be equal to "the number of A-chain's residues plus 1". And it was also strange that the number of first water molecules was equal to "the number of B-chain plus 1" I thought it should be equal to "the number of A-chain's residues plus the number of B-chain's residues plus 1" Is it a bug? No, it is the expected output. By default, pdb2gmx does not renumber residues consecutively. This feature was introduced some time ago so that output selections could easily be made in multiple chain molecules like this one. If you want residues renumbered consecutively, either post-process the coordinate files with genconf -renumber or start over and use pdb2gmx -renum. -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] disulfide bond, molecule type
Hi, I'm trying to heat a protein. There are two chains, A-chain and B-chain. Two disulfide bonds are between A-chain and B-chain. As I know, I should let A-chain and B-chain belong to the same [molecule type] in .top file if I want to have the two inter-bonds. So, I delete the TER line between A-chain and B-chain in .pdb file. And then I use "pdb2gmx -chainsep interactive" on it . I got the two bonds successfully. But after heating, the length of A-chain and B-chain in VMD was changed. The number of residues in A-chain increase and the ones of B-chain decrease. It means some residues move from B-chain to A-chain. How should I prevent this kind of error happen. Besides, I found even though I only have protein_A which consist both of A-chain and B-chain. The number of first residue of B-chain is started from 1 in .gro file. I thought it should be equal to "the number of A-chain's residues plus 1". And it was also strange that the number of first water molecules was equal to "the number of B-chain plus 1" I thought it should be equal to "the number of A-chain's residues plus the number of B-chain's residues plus 1" Is it a bug? 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
