Re: [gmx-users] so difficult problem
Dear justin I generated it by PRODRG server,and modifying Protein.top as it is in ENZYME/DRUG tutorial. Actually I don't know where is problem. Ok,I will modify my EM parameter to do a good energy minimization. Thanks in advance On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how can i do Making ad hoc changes to coordinates is a bad idea. What you might gain by relaxing nonbonded forces you might strain within the molecule (bonded interactions). Proper energy minimization should resolve any high forces. What is your ligand? How did you generate its topology? Poor parameters can also give bad contacts and forces. -Justin thanks in advance On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277
Re: [gmx-users] so difficult problem
Sory. My ligand is Citalopram(a drug) On Mon, Jan 17, 2011 at 1:35 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear justin I generated it by PRODRG server,and modifying Protein.top as it is in ENZYME/DRUG tutorial. Actually I don't know where is problem. Ok,I will modify my EM parameter to do a good energy minimization. Thanks in advance On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how can i do Making ad hoc changes to coordinates is a bad idea. What you might gain by relaxing nonbonded forces you might strain within the molecule (bonded interactions). Proper energy minimization should resolve any high forces. What is your ligand? How did you generate its topology? Poor parameters can also give bad contacts and forces. -Justin thanks in advance On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090
Re: [gmx-users] so difficult problem
mohsen ramezanpour wrote: Dear justin I generated it by PRODRG server,and modifying Protein.top as it is in ENZYME/DRUG tutorial. Actually I don't know where is problem. Ok,I will modify my EM parameter to do a good energy minimization. Back up and start over. PRODRG topologies (especially for a molecule as complex as yours) are generally of very poor quality. Garbage in, garbage out. Even if you manage to get the simulations running I wouldn't necessarily trust the outcome. Please see the paper linked from: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips You may want to re-think the force field entirely. Gromos96 parameter sets are not particularly versatile when it comes to the types of functional groups that can be described, making correct topology generation somewhat difficult for most drug molecules. -Justin Thanks in advance On Sat, Jan 15, 2011 at 6:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how can i do Making ad hoc changes to coordinates is a bad idea. What you might gain by relaxing nonbonded forces you might strain within the molecule (bonded interactions). Proper energy minimization should resolve any high forces. What is your ligand? How did you generate its topology? Poor parameters can also give bad contacts and forces. -Justin thanks in advance On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote:
Re: [gmx-users] so difficult problem
I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how can i do thanks in advance On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen
Re: [gmx-users] so difficult problem
mohsen ramezanpour wrote: I checked this one but it did not solve the problem. Actually I did in your way and I found the force is very high on one atom of my ligand,C12. I checked it's structure with pymol,it 's situation was normal. can I change it's coordinate a few? I think it can make force less. please let me know how can i do Making ad hoc changes to coordinates is a bad idea. What you might gain by relaxing nonbonded forces you might strain within the molecule (bonded interactions). Proper energy minimization should resolve any high forces. What is your ligand? How did you generate its topology? Poor parameters can also give bad contacts and forces. -Justin thanks in advance On Wed, Jan 12, 2011 at 3:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430
Re: [gmx-users] so difficult problem
Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the e... -- 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 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 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] so difficult problem
Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.4 0.1137 12.9330 0.1090 5291 5293 59.1 0.1422 32.1605 0.1390 5291 5292 103.5 0.1096 9.8747 0.1090 5289 5291 89.5 0.1383 39.2022 0.1390 5289 5290 85.7 0.1410 43.8439 0.1360 5289 5287 85.4 0.1426 44.0196 0.1390 5287 5288 90.2 0.1091 1.5178 0.1090 5285 5287 88.7 0.1391 1.9186 0.1390 5285 5286 41.8 0.1092 0.1322 0.1090 5284 5293 87.2 0.1429 21.7425 0.1390 5284 5285 92.4 0.1393 2.0880 0.1390 5277 5278 79.1 0.1532 0.5213 0.1530 5276 5284 63.0 0.1394 1.8946 0.1390 5276 5277 79.2 0.1534 0.7278 0.1530 5276 5275 79.9 0.1432 0.6036 0.1430 5274 5275 82.0 0.1431 0.3189 0.1430 5276 5272 82.1 0.1393 0.6113 0.1390 5272 5273 74.2 0.1333 0.2251 0.1330 5272 5270 77.7 0.1332 0.2428 0.1330 5270 5271 46.5 0.1091 0.1682 0.1090 5268 5270 36.9 0.1391 0.1854 0.1390 5273 5266 41.4 0.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the e... -- gmx-users mailing list gmx-us...@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 list gmx-us...@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 list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D.
Re: [gmx-users] so difficult problem
Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the e... -- 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 mailing listgmx-users@gromacs.org
Re: [gmx-users] so difficult problem
Hi Mohsen, You started off with a pdb file or so. What commands (full command lines) did you issue to get to the point where you are?... Tsjerk On Wed, Jan 12, 2011 at 11:37 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.4 0.1137 12.9330 0.1090 5291 5293 59.1 0.1422 32.1605 0.1390 5291 5292 103.5 0.1096 9.8747 0.1090 5289 5291 89.5 0.1383 39.2022 0.1390 5289 5290 85.7 0.1410 43.8439 0.1360 5289 5287 85.4 0.1426 44.0196 0.1390 5287 5288 90.2 0.1091 1.5178 0.1090 5285 5287 88.7 0.1391 1.9186 0.1390 5285 5286 41.8 0.1092 0.1322 0.1090 5284 5293 87.2 0.1429 21.7425 0.1390 5284 5285 92.4 0.1393 2.0880 0.1390 5277 5278 79.1 0.1532 0.5213 0.1530 5276 5284 63.0 0.1394 1.8946 0.1390 5276 5277 79.2 0.1534 0.7278 0.1530 5276 5275 79.9 0.1432 0.6036 0.1430 5274 5275 82.0 0.1431 0.3189 0.1430 5276 5272 82.1 0.1393 0.6113 0.1390 5272 5273 74.2 0.1333 0.2251 0.1330 5272 5270 77.7 0.1332 0.2428 0.1330 5270 5271 46.5 0.1091 0.1682 0.1090 5268 5270 36.9 0.1391 0.1854 0.1390 5273 5266 41.4 0.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the e... -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] so difficult problem
On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com mailto:ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb
Re: [gmx-users] so difficult problem
Dear yes,I did my work with pdb files. these are my commands after generating complex.gro and complex.top(according to Enzyme/Drug tutorial) editconf -f complex.gro -o box.pdb -d 1.0 -angles 90 90 90 ;for generating a typical rectangular box editconf -f box.pdb -o first-box -vec 5 5 20 -translate 0 0 4 ;to make a rectangular box with wanted length editconf -f first-box -o second-box -rotate 0 0 6;to rotate box around it's z axis editconf -f second-box -o third-box -rotate 0 127 0 ;to rotate box around it's y axis genbox -cp third-box -cs spc216 -p complex.top -o solvent.pdb ;to make solvate grompp -f ion.mdp -c solvent.pdb -o solvent-ion.tpr -p complex.top genion -s solvent-ion.tpr -o solvent-ion.pdb -p complex.top -neutral -nn 3 grompp -f minim.mdp -c solvent-ion.pdb -o solvent-ion-EM.tpr -p complex.top mdrun-v -deffnm solvent-ion-EM grompp -f npt.mdp -c solvate-ion-EM.pdb -o NPT.tpr mdrun-v -deffnm NPT On Wed, Jan 12, 2011 at 2:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, You started off with a pdb file or so. What commands (full command lines) did you issue to get to the point where you are?... Tsjerk On Wed, Jan 12, 2011 at 11:37 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com
Re: [gmx-users] so difficult problem
On Wed, Jan 12, 2011 at 2:59 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 12/01/2011 9:37 PM, mohsen ramezanpour wrote: Dear Dr,Tsjerk I want to estimate protein-drug binding free energy. I am using umbrella sampling for this mean. my drug is inside of a hole in protein. then I have to rotate my system to can fit the pulling line along one box axis. besides I have to pull drug not at direction which connect COM of protein and drug,but it is better to pull it along line which connects drug to a residue inside of hole. I would 1) take my starting bound configuration, 2) strip away anything except the protein complex, 3) delete the box information, 4) rotate the complex with editconf until I was happy with its orientation, 5) then generate a suitable box around that orientation, 6) do EM 7) solvate and neutralize 8) do EM 9) etc. Mark Dear Mark thanks for your reply I will check this ways too. I rotated box with editconf ,solvated system with genbox,neutralized with genion, now I want to generate NPT and then generating configuration as umbrella sampling tutorial. On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Mohsen, You're doing something terribly wrong. But why you want to do what you attempt eludes me. Maybe it helps if you give an explanation of what you want, in stead of what doesn't work. In addition, give the set of commands that bring you up to this point, and not only the output of mdrun. That way we can probably see where you go astray. Cheers, Tsjerk On Wed, Jan 12, 2011 at 10:55 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion. I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.40.1137 12.9330 0.1090 5291 5293 59.10.1422 32.1605 0.1390 5291 5292 103.50.1096 9.8747 0.1090 5289 5291 89.50.1383 39.2022 0.1390 5289 5290 85.70.1410 43.8439 0.1360 5289 5287 85.40.1426 44.0196 0.1390 5287 5288 90.20.1091 1.5178 0.1090 5285 5287 88.70.1391 1.9186 0.1390 5285 5286 41.80.1092 0.1322 0.1090 5284 5293 87.20.1429 21.7425 0.1390 5284 5285 92.40.1393 2.0880 0.1390 5277 5278 79.10.1532 0.5213 0.1530 5276 5284 63.00.1394 1.8946 0.1390 5276 5277 79.20.1534 0.7278 0.1530 5276 5275 79.90.1432 0.6036 0.1430 5274 5275 82.00.1431 0.3189 0.1430 5276 5272 82.10.1393 0.6113 0.1390 5272 5273 74.20.1333 0.2251 0.1330 5272 5270 77.70.1332 0.2428 0.1330 5270 5271 46.50.1091 0.1682 0.1090 5268 5270 36.90.1391 0.1854 0.1390 5273 5266 41.40.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 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 Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4,
Re: [gmx-users] so difficult problem
Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the exact command lines ? On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: please let me know more. I am new with gromacs. did I understand correctly?You say me to use from trjconv at first and then from editconf? I want to keep fix my molecule and rotate my box to locate in awanted direction. waht can I do? because when I rotate the box my molecule totally is located out of box,but protein and ligand are connected as the first state and I think my molecule has not broken. Thanks in advance On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey kgp.a...@gmail.com wrote: May be you broke the molecule while using editconf. Try to fix the periodicity by trjconv and then use it. On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.comwrote: There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287
Re: [gmx-users] so difficult problem
Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2 Cheers, Tsjerk On Jan 6, 2011 7:22 PM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey kgp.a...@gmail.com wrote: Could you post the e... -- 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 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] so difficult problem
Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390 5276 5277 68.40.1543 90.8248 0.1530 5276 5275 39.50.1439 72.5216 0.1430 5274 5275 103.70.1436 21.6028 0.1430 5273 5274 108.50.1394 3.3421 0.1390 5276 5272 45.70.1402 80.6795 0.1390 5272 5273 127.30.1340 14.2401 0.1330 5272 5270 69.80.1336 12.6250 0.1330 5270 5271 113.30.1092 0.2530 0.1090 5268 5270 104.60.1391 0.2718 0.1390 5268 5269 44.40.1091 0.1636 0.1090 5273 5266 58.50.1342 14.0125 0.1330 5265 5268 36.50.1394 0.1769 0.1390 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2# Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965 which is larger than the 1-4 table size 2.400 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 Please let me know the solution. Thanks in advance -- 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] so difficult problem
There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390 5276 5277 68.40.1543 90.8248 0.1530 5276 5275 39.50.1439 72.5216 0.1430 5274 5275 103.70.1436 21.6028 0.1430 5273 5274 108.50.1394 3.3421 0.1390 5276 5272 45.70.1402 80.6795 0.1390 5272 5273 127.30.1340 14.2401 0.1330 5272 5270 69.80.1336 12.6250 0.1330 5270 5271 113.30.1092 0.2530 0.1090 5268 5270 104.60.1391 0.2718 0.1390 5268 5269 44.40.1091 0.1636 0.1090 5273 5266 58.50.1342 14.0125 0.1330 5265 5268 36.50.1394 0.1769 0.1390 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2# Wrote pdb files with previous and current coordinates step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965 which is larger than the 1-4 table size 2.400 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 Please let me know the solution.
Re: [gmx-users] so difficult problem
I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.com wrote: There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390 5276 5277 68.40.1543 90.8248 0.1530 5276 5275 39.50.1439 72.5216 0.1430 5274 5275 103.70.1436 21.6028 0.1430 5273 5274 108.50.1394 3.3421 0.1390 5276 5272 45.70.1402 80.6795 0.1390 5272 5273 127.30.1340 14.2401 0.1330 5272 5270 69.80.1336 12.6250 0.1330 5270 5271 113.30.1092 0.2530 0.1090 5268 5270 104.60.1391 0.2718 0.1390 5268 5269 44.40.1091 0.1636 0.1090 5273 5266 58.50.1342 14.0125 0.1330 5265 5268 36.50.1394 0.1769 0.1390 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2# Wrote pdb files with previous and current coordinates step 0Warning: 1-4
Re: [gmx-users] so difficult problem
May be you broke the molecule while using editconf. Try to fix the periodicity by trjconv and then use it. On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.com wrote: There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390 5276 5277 68.40.1543 90.8248 0.1530 5276 5275 39.50.1439 72.5216 0.1430 5274 5275 103.70.1436 21.6028 0.1430 5273 5274 108.50.1394 3.3421 0.1390 5276 5272 45.70.1402 80.6795 0.1390 5272 5273 127.30.1340 14.2401 0.1330 5272 5270 69.80.1336 12.6250 0.1330 5270 5271 113.30.1092 0.2530 0.1090 5268 5270 104.60.1391 0.2718 0.1390 5268 5269 44.40.1091 0.1636 0.1090 5273 5266 58.50.1342 14.0125 0.1330 5265 5268 36.50.1394 0.1769 0.1390
Re: [gmx-users] so difficult problem
please let me know more. I am new with gromacs. did I understand correctly?You say me to use from trjconv at first and then from editconf? I want to keep fix my molecule and rotate my box to locate in awanted direction. waht can I do? because when I rotate the box my molecule totally is located out of box,but protein and ligand are connected as the first state and I think my molecule has not broken. Thanks in advance On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey kgp.a...@gmail.com wrote: May be you broke the molecule while using editconf. Try to fix the periodicity by trjconv and then use it. On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.com wrote: There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390 5276 5277 68.40.1543 90.8248 0.1530 5276 5275 39.50.1439 72.5216 0.1430 5274 5275 103.70.1436
Re: [gmx-users] so difficult problem
Could you post the exact command lines ? On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: please let me know more. I am new with gromacs. did I understand correctly?You say me to use from trjconv at first and then from editconf? I want to keep fix my molecule and rotate my box to locate in awanted direction. waht can I do? because when I rotate the box my molecule totally is located out of box,but protein and ligand are connected as the first state and I think my molecule has not broken. Thanks in advance On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey kgp.a...@gmail.com wrote: May be you broke the molecule while using editconf. Try to fix the periodicity by trjconv and then use it. On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: I generated my .top and .gro file as drug/enzyme tutorial. I used PRODRG to generate them. I could pass all of steps in UMbrella sampling tutorial with these files,without any warning or error. the one thing I changed is rotating box with editconf. On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey kgp.a...@gmail.comwrote: There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I am using this .mdp file and I recived the below warnings,I can't solve that. title= NPT define = integrator = md tinit= 0 dt = 0.002 nsteps = 50 nstcomm = 1 comm-grps= protein non-protein niter= 20 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc-precision= 1000 xtc_grps = protein non-protein energygrps = Protein non-protein nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no tcoupl = Nose-hoover tc-grps = Protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 annealing= no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-warnangle = 30 morse= no my sytem is protein-ligand,I want to generate a NPT. the result was: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 50 steps, 1000.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 41.70.1143 0.1261 0.1140 5293 5294 82.70.1221 2612.9744 0.1090 5291 5293 77.20.1517 6082.6147 0.1390 5291 5292 101.00.1117 1518.6106 0.1090 5289 5291 87.70.1353 6891.8911 0.1390 5289 5290 88.40.1437 7529.4878 0.1360 5289 5287 88.40.1456 7540.4873 0.1390 5287 5288 89.70.1092 381.5114 0.1090 5285 5287 92.30.1395 354.9220 0.1390 5285 5286 123.80.1101 44.8448 0.1090 5284 5293 89.00.1478 4605.1763 0.1390 5284 5285 79.30.1402 173.5627 0.1390 5278 5279 78.90.1529 1.1270 0.1530 5277 5278 122.90.1545 13.1423 0.1530 5276 5284 84.90.1422 159.0098 0.1390
