[gmx-users] Re: \\[gmx\\-users\\] The energy minimization\\.\\.\\.\\.
As i say keep things to the list please. With regards to the files no as you should be able to fix the problem on your own as this will help you more in the long run. Try redoing every step making sure you do it correctly (especially the editing of the .rtp file) Tom --On 18 August 2007 10:58 +0800 MoJie Duan <[EMAIL PROTECTED]> wrote: Hi,tom: Thank you for you help! Could you provid me the run file about the EM of my ATP molecule? (the .gro, .top, and .gro&.top files after editconf, the .tpr after grompp... maybe also the ff**.trp and ff*.hdb you used). I will check which step have problems. And if i solve this problem, i will introduce my experience of resolving this problem in gmx-user for the beginner. Best regards! Duan Hi I just quickly checked and your ATP pdb file works fine for me (it did have some weird characters in it that i had to delete, not sure if this was caused by pasting it into an email). I should point out that this pdb file is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell you this if you modified your .rtp file correctly). See any of the GROMOS96 .rtp file ATP entries for the hydrogens you have missed that still are included in a united atom ff. Also your .mdp parameters work fine with your pdb file so i have no idea what is going wrong when you try! Check you have modified the .rtp file correctly and are supplying sensible commands to pdb2gmx/editconf/grompp/mdrun are the last things i can suggest. Good luck Tom --On 18 August 2007 08:17 +0800 MoJie Duan wrote: Hi,Tom: Thank you for your reply! Before the minimization, I just change the atoms name of ATP, so it can coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1 also changed, each atom have a three-letter name). My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz coordinates of ATP molecule from the a .pdb file of a protein, as following: ___ HETATM 7577 PG ATP 800 -4.997 4.425 -2.604 1.00 & gt; 33.08 P HETATM 7578 O1G ATP 800 -5.685 5.603 -1.764 1.00 33.76 O HETATM 7579 O2G ATP 800 -3.427 4.765 -2.665 1.00 32.63 0; O HETATM 7580 O3G ATP 800 -5.273 3.100 -1.967 1.00 33.16 O HETATM 7581 PB ATP 800 -5.173 3.787 -5.388 1.00 34.37 P HETATM 7582 O1B ATP 800 -3.985 4.318 -6.120 1.00 33.33 O HETATM 7583 O2B ATP 800 -5.232 2.335 -5.045 1.00 33.33 O HETATM 7584 O3B ATP 800 -5.529 4.675 -4.089 1.00 33.22 O HETATM 7585 PA ATP 800 -7.773 3.348 -6.436 1.00 35.04 P HETATM 7586 O1A ATP 800 -8.260 2.720 -5.177 1.00 33.60 O HETATM 7587 O2A ATP 800 -7.501 2.503 -7.632 1.00 32.64 O HETATM 7588 O3A ATP 800 -6.483 4.274 -6.168 1.00 34.07 O HETATM 7589 O5' ATP 800 -8.787 4.518 0; -6.833 1.00 36.40 O HETATM 7590 C5' ATP 800 -8.403 5.464 -7.846 1.00 39.10 C HETATM 7591 C4' ATP 800 -9.604 6.315 -8.269 1.00 41.61 C HETATM 7592 O4' ATP 800 -10.793 5.471 -8.462 1.00 42.22 O HETATM 7593 C3' ATP 800 -9.937 7.303 -7.152 1.00 41.81 C HETATM 7594 O3' ATP 800 -10.228 8.5 59 -7.756 1.00 43.61 O HETATM 7595 C2' ATP 800 -11.191 6.724 -6.514 1.00 42.05 C HETATM 7596 O2' ATP 800 -12.023 7.764 -6.036 1.00 41.49 O HETATM 7597 C1' ATP 800 -11.875 6.025 -7.679 1.00 42.90 C HETATM 7598 N9 ATP 800 -12.608 4.832 -7.218 1.00 43.53 N HETATM 7599 C8 ATP 800 -12.077 3. 810 -6.547 1.00 43.35 C HETATM 7600 N7 ATP 800 -13.023 2.904 -6.309 1.00 44.02 N HETATM 7601 C5 ATP 800 -14.162 3.341 -6.835 1.00 44.22 C HETATM 7602 C6 ATP 800 -15.461 2.828 -6.899 1.00 44.02 C HETATM 7603 N6 ATP 800 -15.751 1.647 -6.351 1.00 43.35 N HETATM 7604 N1 ATP 800 -16.41 4 3.547 -7.525 1.00 43.25 N HETATM 7605 C2 ATP 800 -16.125 4.717 -8.076 1.00 43.37 C HETATM 7606 N3 ATP 800 -14.902 5.230 -8.032 1.00 43.76 N HETATM 7607 C4 ATP 800 -13.901 4.571 -7.417 1.00 44.09 C and then changed the atoms name: HETATM 7577 APG ATP 800 -4.997 4.425 -2.604& #160; 1.00 33.08 P HETATM 7578 OG1 ATP 800 -5.685 5.603 -1.764 1.00 33.76 O HETATM 7579 OG2 ATP 800 -3.427 4.765 -2.665 1.00 32.63 O HETATM 7580 OG3 ATP 800 -5.273 3.100 -1.967 1.00 33.16 O HETATM 7581 APB ATP 800 -5.173 3.787 -5.388 1.00 34.37 P HETATM 7582 OB1 ATP 800 -3.985 4.3 18 -6.120 1.00 33.33 O HETATM 7583 OB2 ATP 800 -5.232 2.335 -5.045 1.00 33.33 O HETATM 7584 OB3 ATP 800 -5.529 4.675 -4.089 1.00 33.22 O HETATM 7585 APA ATP 800 -7.773 3.348 -6.436 1.00 35.04 P HETATM 7586 OA1 ATP 800 -8.260 2.720 -5.177 1.00 33.60 O HETATM 7587 OA2 ATP 800 -7.501 2.503 -7.632 1.00 32.64 O HETATM 7588 OA3 ATP 800 -6.483 4.274 -6.168 1.00 34.07 O HETATM 7589 A5O ATP 800 -8.787 4.518 -6.833 1.00 36.40 O HETATM 7590 A5C ATP 800 -8.403 5.464 -7.846 1.00 39.10 C HETATM 7591 A4C ATP 800 -9.604 6.315 -8.269 1.00 41.61 C HETATM 7592 A4O ATP 800 60; -10.793 5.471 -8.462 1.00 42.22 O HETATM 7593 A3C ATP 800 -9.937 7.303 -7.152 1.00 41.81 C HETATM 7594 A3O ATP 800 -10.228 8.559 -7.756 1.00 43.61 O HETATM 7595 A2C ATP 800 -11.191 6.724 -6.514 1.00 42.05 C HETATM
[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)
Hi Also please keep emails on the list, it helps everyone (you getting more people's opinion than just mine, and people who may have a similar problem in the future) Tom Forwarded Message Date: 18 August 2007 02:29 +0100 From: TJ Piggot <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Subject: Re: \[gmx\-users\] The energy minimization\.\.\.\. Hi I just quickly checked and your ATP pdb file works fine for me (it did have some weird characters in it that i had to delete, not sure if this was caused by pasting it into an email). I should point out that this pdb file is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell you this if you modified your .rtp file correctly). See any of the GROMOS96 .rtp file ATP entries for the hydrogens you have missed that still are included in a united atom ff. Also your .mdp parameters work fine with your pdb file so i have no idea what is going wrong when you try! Check you have modified the .rtp file correctly and are supplying sensible commands to pdb2gmx/editconf/grompp/mdrun are the last things i can suggest. Good luck Tom --On 18 August 2007 08:17 +0800 MoJie Duan <[EMAIL PROTECTED]> wrote: Hi,Tom: Thank you for your reply! Before the minimization, I just change the atoms name of ATP, so it can coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1 also changed, each atom have a three-letter name). My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz coordinates of ATP molecule from the a .pdb file of a protein, as following: ___ HETATM 7577 PG ATP 800 -4.997 4.425 -2.604 1.00 33.08 P HETATM 7578 O1G ATP 800 -5.685 5.603 -1.764 1.00 33.76 O HETATM 7579 O2G ATP 800 -3.427 4.765 -2.665 1.00 32.63 0; O HETATM 7580 O3G ATP 800 -5.273 3.100 -1.967 1.00 33.16 O HETATM 7581 PB ATP 800 -5.173 3.787 -5.388 1.00 34.37 P HETATM 7582 O1B ATP 800 -3.985 4.318 -6.120 1.00 33.33 O HETATM 7583 O2B ATP 800 -5.232 2.335 -5.045 1.00 33.33 O HETATM 7584 O3B ATP 800 -5.529 4.675 -4.089 1.00 33.22 O HETATM 7585 PA ATP 800 -7.773 3.348 -6.436 1.00 35.04 P HETATM 7586 O1A ATP 800 -8.260 2.720 -5.177 1.00 33.60 O HETATM 7587 O2A ATP 800 -7.501 2.503 -7.632 1.00 32.64 O HETATM 7588 O3A ATP 800 -6.483 4.274 -6.168 1.00 34.07 O HETATM 7589 O5' ATP 800 -8.787 4.518 0; -6.833 1.00 36.40 O HETATM 7590 C5' ATP 800 -8.403 5.464 -7.846 1.00 39.10 C HETATM 7591 C4' ATP 800 -9.604 6.315 -8.269 1.00 41.61 C HETATM 7592 O4' ATP 800 -10.793 5.471 -8.462 1.00 42.22 O HETATM 7593 C3' ATP 800 -9.937 7.303 -7.152 1.00 41.81 C HETATM 7594 O3' ATP 800 -10.228 8.5 59 -7.756 1.00 43.61 O HETATM 7595 C2' ATP 800 -11.191 6.724 -6.514 1.00 42.05 C HETATM 7596 O2' ATP 800 -12.023 7.764 -6.036 1.00 41.49 O HETATM 7597 C1' ATP 800 -11.875 6.025 -7.679 1.00 42.90 C HETATM 7598 N9 ATP 800 -12.608 4.832 -7.218 1.00 43.53 N HETATM 7599 C8 ATP 800 -12.077 3. 810 -6.547 1.00 43.35 C HETATM 7600 N7 ATP 800 -13.023 2.904 -6.309 1.00 44.02 N HETATM 7601 C5 ATP 800 -14.162 3.341 -6.835 1.00 44.22 C HETATM 7602 C6 ATP 800 -15.461 2.828 -6.899 1.00 44.02 C HETATM 7603 N6 ATP 800 -15.751 1.647 -6.351 1.00 43.35 N HETATM 7604 N1 ATP 800 -16.41 4 3.547 -7.525 1.00 43.25 N HETATM 7605 C2 ATP 800 -16.125 4.717 -8.076 1.00 43.37 C HETATM 7606 N3 ATP 800 -14.902 5.230 -8.032 1.00 43.76 N HETATM 7607 C4 ATP 800 -13.901 4.571 -7.417 1.00 44.09 C and then changed the atoms name: HETATM 7577 APG ATP 800 -4.997 4.425 -2.604& #160; 1.00 33.08 P HETATM 7578 OG1 ATP 800 -5.685 5.603 -1.764 1.00 33.76 O HETATM 7579 OG2 ATP 800 -3.427 4.765 -2.665 1.00 32.63 O HETATM 7580 OG3 ATP 800 -5.273 3.100 -1.967 1.00 33.16 O HETATM 7581 APB ATP 800 -5.173 3.787 -5.388 1.00 34.37 P HETATM 7582 OB1 ATP 800 -3.985 4.3 18 -6.120 1.00 33.33 O HETATM 7583 OB2 ATP 800 -5.232 2.335 -5.045 1.00 33.33 O HETATM 7584 OB3 ATP 800 -5.529 4.675 -4.089 1.00 33.22 O HETATM 7585 APA ATP 800 -7.773 3.348 -6.4
Re: [gmx-users] The energy minimization....
The end structure is the same as the start because gromacs cannot find a lower energy structure than the initial one. This indicates something severely wrong, either with the topology or starting structure. You could get a better idea of what's going on by telling gromacs to output structures every step in the minimisation, and examining these so you can actually observe what is happening to your ATP. I've occasionally seen similar results from minimisation, but only after doing something REALLY bad, like precisely overlaying two molecules on the same coordinates. Debugging something like this is probably something only you are going to be able to do, as there are just so many potential ways a suitably, uh, imaginative user can mess things up. - Original Message From: MoJie Duan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, August 17, 2007 11:15:40 AM Subject: Re: [gmx-users] The energy minimization Hi, Mark: I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution). There are following problems: 1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning): -- Getting Loaded... Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= & #160;200 Step=0, Dmax= 1.0e-02 nm, Epot= 1.06678e+05 Fmax= 3.63368e+06, atom= 26 Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 3.63313e+06, ^^^ atom= 26 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1. Potential Energy = 1.0667836e+05 Maximum for ce = 3.6336775e+06 on atom 26 Norm of force =nan ___ 2. in the full MD simulation, the "warning" coming, the messages is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.881911 (between atoms 27 and 28) rms nan bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 27 28 90.00.1610 0.3030 0.1610 Wrote pdb files with previous and current coordinates step 2490, remaining runtime: 0 s & #160; Writing final coordinates. Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1# step 2500, remaining runtime: 0 s __ And in the ".gro" file after this step, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal? Thank you very much! Duan >MoJie Duan wrote: > > >So look at your structures like I said last time! I'm not her e to give > > >my valuable time giving free advice in order to have it ignored... > > Thank you very much for your kindness and patience. Maybe sometimes my > > questions seems to be silly and boring, my knowledge about GROMACS is > >really lack, sorry. > > >Actually, I really cannot understand what you said yesterday. Did you > >mean is there any difference between the atom coordinates of ATP before- > >and after- minimization? > There would normally be some differences visible. If your topology was > badly broken, then you would usually see where it was broken. > >I found there are not any difference between > >these two structure. > >(There are also not any obvious collision between atoms of ATP when > >represent it by Rasmol) > OK, so that means your structure is in a flat area of the potential > surface defined by your topology. If the topology is sound, then you're > in business. > My first recommendation was to minimize and/or equilibrate these > structures on their own, and now I suggest doing them also in solvent. > This will help you eliminate sources of problems and guide you to > what the real pro
Re: [gmx-users] The energy minimization....
Hi you need to explain in detail what steps you are doing before the minimisation and also what parameters you are using in your .mdp file because i have just run a minimisation of ATP (in water) to test the topology in the GROMOS96 ff and it works fine for me, so there must be a problem in one of your setup steps or your simulation parameters. Tom --On Friday, August 17, 2007 18:15:40 +0800 MoJie Duan <[EMAIL PROTECTED]> wrote: Hi, Mark: I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution). There are following problems: 1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning): -- Getting Loaded... Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1# Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = & #160; 200 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.06678e+05 Fmax= 3.63368e+06, atom= 26 Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 3.63313e+06, ^^^ atom= 26 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1. Potential Energy = 1.0667836e+05 Maximum for ce = 3.6336775e+06 on atom 26 Norm of force = nan ___ 2. in the full MD simulation, the "warning" coming, the messages is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.881911 (between atoms 27 and 28) rms nan bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 27 28 90.0 0.1610 0.3030 0.1610 Wrote pdb files with previous and current coordinates step 2490, remaining runtime: 0 s & #160; Writing final coordinates. Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1# step 2500, remaining runtime: 0 s __ And in the ".gro" file after this step, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal? Thank you very much! Duan MoJie Duan wrote: > > So look at your structures like I said last time! I'm not her e to > > give my valuable time giving free advice in order to have it > > ignored... > Thank you very much for your kindness and patience. Maybe sometimes my > questions seems to be silly and boring, my knowledge about GROMACS is > really lack, sorry. > Actually, I really cannot understand what you said yesterday. Did you > mean is there any difference between the atom coordinates of ATP > before- and after- minimization? There would normally be some differences visible. If your topology was badly broken, then you would usually see where it was broken. > I found there are not any difference between > these two structure. > (There are also not any obvious collision between atoms of ATP when > represent it by Rasmol) OK, so that means your structure is in a flat area of the potential surface defined by your topology. If the topology is sound, then you're in business. My first recommendation was to minimize and/or equilibrate these structures on their own, and now I suggest doing them also in solvent. This will help you eliminate sources of problems and guide you to what the real problem is. Divide and conquer... That's fine, then. OK, so here's your problem. Work out what's breaking and why. Read the error messages and look at the structures. Understand what each of > your .mdp file options does. Mark -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
Hi, Mark:I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution).There are following problems:1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning):--Getting Loaded...Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)Loaded with MoneyBack Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = & #160; 200Step= 0, Dmax= 1.0e-02 nm, Epot= 1.06678e+05 Fmax= 3.63368e+06, atom= 26Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 3.63313e+06, ^^^atom= 26Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1Double precision normally gives you higher accuracy.writing lowest energy coordinates.Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax < 1.Potential Energy = 1.0667836e+05Maximum for ce = 3.6336775e+06 on atom 26Norm of force = nan___2. in the full MD simulation, the "warning" coming, the messages is:Step 0, time 0 (ps) LINCS WARNINGrelative constraint deviation after LINCS:max 0.881911 (between atoms 27 and 28) rms nanbonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 27 28 90.0 0.1610 0.3030 0.1610Wrote pdb files with previous and current coordinatesstep 2490, remaining runtime: 0 s & #160; Writing final coordinates.Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#step 2500, remaining runtime: 0 s __And in the ".gro" file after this step, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal?Thank you very much!Duan<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]>>MoJie Duan wrote:> > >So look at your structures like I said last time! I'm not her e to give> > >my valuable time giving free advice in order to have it ignored...> > Thank you very much for your kindness and patience. Maybe sometimes my > > questions seems to be silly and boring, my knowledge about GROMACS is > >really lack, sorry.> > >Actually, I really cannot understand what you said yesterday. Did you > >mean is there any difference between the atom coordinates of ATP before- > >and after- minimization?> There would normally be some differences visible. If your topology was> badly broken, then you would usually see where it was broken.> >I found there are not any difference between > >these two structure.> >(There are also not any obvious collision between atoms of ATP when > >represent it by Rasmol)> OK, so that means your structure is in a flat area of the potential> surface defined by your topology. If the topology is sound, then you're> in business.> My first recommendation was to minimize and/or equilibrate these> structures on their own, and now I suggest doing them also in solvent.> This will help you eliminate sources of problems and guide you to > what the real problem is. Divide and conquer...> That's fine, then.> OK, so here's your problem. Work out what's breaking and why. Read the> error messages and look at the structures. Understand what each of > your .mdp file options does.Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
MoJie Duan wrote: > >So look at your structures like I said last time! I'm not here to give > >my valuable time giving free advice in order to have it ignored... > > Thank you very much for your kindness and patience. Maybe sometimes my > questions seems to be silly and boring, my knowledge about GROMACS is > really lack, sorry. > > Actually, I really cannot understand what you said yesterday. Did you > mean is there any difference between the atom coordinates of ATP before- > and after- minimization? There would normally be some differences visible. If your topology was badly broken, then you would usually see where it was broken. > I found there are not any difference between > these two structure. > (There are also not any obvious collision between atoms of ATP when > represent it by Rasmol) OK, so that means your structure is in a flat area of the potential surface defined by your topology. If the topology is sound, then you're in business. > > >[EMAIL PROTECTED] wrote: > > > > >To reply to a list email, just reply as you would to any other email. > > > > > > >The .top succeeded in minimizing the solvated structure, so that's a > > >good start. I think I can see that I was being too subtle for you > > >earlier with my suggestion that you think about observables that would > > >tell you whether your topology was working. Have you looked at the > > >before- and after-minimization structures to see whether they make > > >sense according to your training at recognizing chemical structures > > >that will be energy minima? If all of your components look > reasonable post-minimization on their own, > what means? My first recommendation was to minimize and/or equilibrate these structures on their own, and now I suggest doing them also in solvent. This will help you eliminate sources of problems and guide you to what the real problem is. Divide and conquer... > > > and there were no significant warnings > > >or errors from grompp then your topolog ies probably are OK too. > ^just like I said in last email, there > are not any warnning and error from grompp. That's fine, then. > > >Thenyou should go back and approach your original problem of getting > > >working topology f or your combination system. > I cannot run the > full MD SImulation for ATP individually, so I think maybe there are > something problem with it (I used the same minim.mdp can successfully do > the energy minimization of the protein individually). I really confused. OK, so here's your problem. Work out what's breaking and why. Read the error messages and look at the structures. Understand what each of your .mdp file options does. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
><[EMAIL PROTECTED]><[EMAIL PROTECTED]>So look at your structures like I said last time! I'm not here to give>my valuable time giving free advice in order to have it ignored...Thank you very much for your kindness and patience. Maybe sometimes my questions seems to be silly and boring, my knowledge about GROMACS is really lack, sorry.Actually, I really cannot understand what you said yesterday. Did you mean is there any difference between the atom coordinates of ATP before- and after- minimization? I found there are not any difference between these two structure.(There are also not any obvious collision between atoms of ATP when represent it by Rasmol) > >[EMAIL PROTECTED] wrote:> > >To reply to a list email, just reply as you would to any other email.> > > >The .top succeeded in minimizing the solvated structure, so that's a> >good start. I think I can see that I was being too subtle for you> >earlier with my suggestion that you think about observables that would> >tell you whether your topology was working. Have you looked at the> >before- and after-minimization structures to see whether they make > >sense according to your training at recognizing chemical structures > >that will be energy minima? If all of your components look reasonable post-minimization on their own, what means?> > and there were no significant warnings> >or errors from grompp then your topolog ies probably are OK too. ^just like I said in last email, there are not any warnning and error from grompp.> >Thenyou should go back and approach your original problem of getting > >working topology f or your combination system. I cannot run the full MD SImulation for ATP individually, so I think maybe there are something problem with it (I used the same minim.mdp can successfully do the energy minimization of the protein individually). I really confused.> > >Mark<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]> ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
MoJie Duan wrote: > Mark: > Thank you for your reply! > I have checked my topology file of the ATP, I think there isn't any > problem with it. When I do the grompp (only use the ATP molecule), there > is not any warning and error, it stopped at 14th step, and return the > following messege: > > Step=0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, > atom= 421 > Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 1.59347e+04, > atom= 4214 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1 > > it's really strange for "Epot = nan". I think maybe there are something > wrong with it even it said "Converged to machine precision". > But when I do the full MD Simulation (not energy minimization), the > program said "Fatal error:Number of grid cells is zero. Probably the > system and box collapse d"!!! (there also isnot any warning and error in > grompp). I think the problem maybe caused by the energy minimization > step, but I really don't know why! So look at your structures like I said last time! I'm not here to give my valuable time giving free advice in order to have it ignored... > >[EMAIL PROTECTED] wrote: > > >To reply to a list email, just reply as you would to any other email. > > > >The .top succeeded in minimizing the solvated structure, so that's a > >good start. I think I can see that I was being too subtle for you > >earlier with my suggestion that you think about observables that would > >tell you whether your topology was working. Have you looked at the > >before- and after-minimization structures to see whether they make > >sense according to your training at recognizing chemical structures > >that will be energy minima? If all of your components look reasonable > >post-minimization on their own, and there were no significant warnings > >or errors from grompp then your topolog ies probably are OK too. Then > >you should go back and approach your original problem of getting a > >working topology for your combination system. > > >Mark > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
Mark:Thank you for your reply!I have checked my topology file of the ATP, I think there isn't any problem with it. When I do the grompp (only use the ATP molecule), there is not any warning and error, it stopped at 14th step, and return the following messege:Step= 0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, atom= 421Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 1.59347e+04, atom= 4214Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1it's really strange for "Epot = nan". I think maybe there are something wrong with it even it said "Converged to machine precision".But when I do the full MD Simulation (not energy minimization), the program said "Fatal error:Number of grid cells is zero. Probably the system and box collapse d"!!! (there also isnot any warning and error in grompp). I think the problem maybe caused by the energy minimization step, but I really don't know why!Duan>[EMAIL PROTECTED] wrote:>To reply to a list email, just reply as you would to any other email.>The .top succeeded in minimizing the solvated structure, so that's a>good start. I think I can see that I was being too subtle for you>earlier with my suggestion that you think about observables that would>tell you whether your topology was working. Have you looked at the>before- and after-minimization structures to see whether they make >sense according to your training at recognizing chemical structures >that will be energy minima? If all of your components look reasonable>post-minimization on their own, and there were no significant warnings>or errors from grompp then your topolog ies probably are OK too. Then >you should go back and approach your original problem of getting a >working topology for your combination system.>Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
Quoting [EMAIL PROTECTED]: > Hi, everyone: > I have meet some problem when simulating a protein and ATP complex. The > energy minimization will stop after 14 steps. I had followed Mark's > suggestion, did the protein and ATP eneryg minimization independently, > and found that the protein can finish its minimization correctly, > but the ATP 's minimization stopped after 14 steps. So it seems > that there are something wrong with ATP. And Mark also said "Probably your > topology is broken", what is it means? What should I do now? > Best wishes! > > > == Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://bevanlab.biochem.vt.edu/Pages/Personal/justin/ == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
Hi, I struggled with a similar minimisation problem with NADP (NDPP topology in ffG43a1). Then I got a suggestion from a colleague in Prof. Ho"ltje's group in Dusseldorf, that the atom naming should be changed from eg. AC5* to something with only three characters, eg. C10. I renamed (and only renamed) all the atoms with a unique running number and got rid of the problem. I'm not sure if this will help you but it worked for me. Hope it helps, Sampo [EMAIL PROTECTED] wrote: > http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html > > > > Mark: > I am sorry to disturb you. I'm a beginner of GROMACS and this > "mailing-list" system. I even don't know how to replay a post directly. > And yesterday I haven't seen your replay because the list title changed, > sorry again! > > About the problem, I haven't resolved it yet. The .top file of my ATP > molecule is generated by the pdb2gmx, and the coordinates of each atom > adopted to the pdb file. The force file is ffG43a2. Whether my topology > file of ATP molecule have something wrong? The topology file of ATP as > following: > > ;File '../ATP/ATP.top' was generated > ;By user: root (0) > ;On host: mjduan-desktop > ;At date: Wed Aug 15 16:55:53 2007 > ; > ;This is your topology file > ;"Does All This Money Really Have To Go To Char ity ?" (Rick) > ; > ; Include forcefield parameters > #include "ffG43a2.itp" > > [ moleculetype ] > ; Namenrexcl > Protein 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeBchargeB massB > 1 NR 1ATPAN9 1 -0.214.0067 ; > qtot -0.2 > 2 C 1 60; ATPAC4 10.2 > 12.011 ; qtot 0 > 3 NR 1ATPAN3 2 -0.3614.0067 ; > qtot -0.36 > 4CR1 1ATPAC2 2 0.36 13.019 ; > qtot 0 > 5 NR 1ATPAN1 3 -0.3614.0067 ; > qtot -0.36 > 6 C 1ATPAC6 3 0.36 12.011 ; > qtot 0 > 7 NT 1ATPAN6 4 -0.8314.0067 ; > qtot -0.83 > 8 H 1ATP AH61 4 0.415 1.008 ; > qtot -0.415 > 9 H 1&# 160; ATP AH62 4 0.415 > 1.008 ; qtot 0 > 10 C 1ATPAC5 5 0 12.011 ; > qtot 0 > 11 NR 1ATPAN7 5 -0.3614.0067 ; > qtot -0.36 > 12CR1 1ATPAC8 5 0.36 13.019&# > 160; ; qtot 0 > 13CH1 1ATP AC1* 60.2 13.019 ; > qtot 0.2 > 14 OA 1ATP AO4* 6 -0.3615.9994 ; > qtot -0.16 > 15CH1 1ATP AC4* 6 0.16 13.019 ; > qtot 0 > 16CH1 1ATP AC2* & #160; 7 0.15 > 13.019 ; qtot 0.15 > 17 OA 1ATP AO2* 7 -0.54815.9994 ; > qtot -0.398 > 18 H 1ATP AH2* 7 0.398 1.008 ; > qtot 0 > 19CH1 1ATP AC3* 8 0.15 13.019 ; > qtot 0.15 > 20 &# 160; OA 1ATP AO3* 8 -0.548 > 15.9994 ; qtot -0.398 > 21 H 1ATP AH3* 8 0.398 1.008 ; > qtot 0 > 22CH2 1ATP AC5* 9 0 14.027 ; > qtot 0 > 23 OA 1ATP AO5* 10 -0.36 60; > 15.9994 ; qtot -0.36 > 24 P 1ATPAPA 10 0.70530.9738 ; > qtot 0.345 > 25 OM 1ATP O1PA 10 -0.63515.9994 ; > qtot -0.29 > 26 OM 1ATP O2PA 10 -0.63515.9994 ; > qtot -0.925 > 27 OA 1ATP O3PA &# 160; 11 -0.36 > 15.9994 ; qtot -1.285 > 28 P 1ATPAPB 11 0.70530.9738 ; > qtot -0.58 > 29 OM 1ATP O1PB 11 -0.63515.9994 ; > qtot -1.215 > 30 OM 1ATP O2PB 11 -0.63515.9994 ; > qtot -1.85 > 31 OA &# 160; 1ATP O3PB 12 -0.36 > 15.9994 ; qtot -2.21 > 32 P 1ATPAPG 12 0.6330.9738 ; > qtot -1.58 > 33 OM 1ATP O1PG 12 -0.63515.9994 ; > qtot -2.215 > 34 OM 1ATP O2PG 12 -0.63515.9994 ; > qtot -2.85 > ; 35 OA 1ATP O3PG 12 -0.54815.9994 > ; qtot -3.398 > 36 H 1ATP H3PG 12 0.398 1.008 ; > qtot -3 > > [ bonds ] > ; aiaj functc0c1c2c3 > 1 2 2gb_9 > 1 ; 12 2gb_9 > 113 2gb_21 > 2 3 2gb_11 >
Re: [gmx-users] The energy minimization....
[EMAIL PROTECTED] wrote: > http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html > > > > Mark: > I am sorry to disturb you. I'm a beginner of GROMACS and this > "mailing-list" system. I even don't know how to replay a post directly. > And yesterday I haven't seen your replay because the list title changed, > sorry again! To reply to a list email, just reply as you would to any other email. > About the problem, I haven't resolved it yet. The .top file of my ATP > molecule is generated by the pdb2gmx, and the coordinates of each atom > adopted to the pdb file. The force file is ffG43a2. Whether my topology > file of ATP molecule have something wrong? The topology file of ATP as > following: The .top succeeded in minimizing the solvated structure, so that's a good start. I think I can see that I was being too subtle for you earlier with my suggestion that you think about observables that would tell you whether your topology was working. Have you looked at the before- and after-minimization structures to see whether they make sense according to your training at recognizing chemical structures that will be energy minima? If all of your components look reasonable post-minimization on their own, and there were no significant warnings or errors from grompp then your topologies probably are OK too. Then you should go back and approach your original problem of getting a working topology for your combination system. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The energy minimization....
Hi, Well, think harder about your 'problem'. How hard can it be to solve all terms to reach the nearest local minimum for a system of 36 atoms? You could basically do it by hand! No wonder that you reach convergence to machine precision in 14 steps. Check the archives on 'stepsize too small' and 'convergence to machine precision', etc. Cheers, Tsjerk On 8/16/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html > > > > Mark: > I am sorry to disturb you. I'm a beginner of GROMACS and this "mailing-list" > system. I even don't know how to replay a post directly. And yesterday I > haven't seen your replay because the list title changed, sorry again! > > About the problem, I haven't resolved it yet. The .top file of my ATP > molecule is generated by the pdb2gmx, and the coordinates of each atom > adopted to the pdb file. The force file is ffG43a2. Whether my topology file > of ATP molecule have something wrong? The topology file of ATP as following: > > ;File '../ATP/ATP.top' was generated > ;By user: root (0) > ;On host: mjduan-desktop > ;At date: Wed Aug 15 16:55:53 2007 > ; > ;This is your topology file > ;"Does All This Money Really Have To Go To Char ity ?" (Rick) > ; > ; Include forcefield parameters > #include "ffG43a2.itp" > > [ moleculetype ] > ; Namenrexcl > Protein 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > 1 NR 1ATPAN9 1 -0.214.0067 ; qtot > -0.2 > 2 C 1 60; ATPAC4 10.2 12.011 > ; qtot 0 > 3 NR 1ATPAN3 2 -0.3614.0067 ; qtot > -0.36 > 4CR1 1ATPAC2 2 0.36 13.019 ; qtot > 0 > 5 NR 1ATPAN1 3 -0.3614.0067 ; qtot > -0.36 > 6 C 1ATPAC6 3 0.36 12.011 ; qtot > 0 > 7 NT 1ATPAN6 4 -0.8314.0067 ; qtot > -0.83 > 8 H 1ATP AH61 4 0.415 1.008 ; qtot > -0.415 > 9 H 1&# 160; ATP AH62 4 0.415 1.008 > ; qtot 0 > 10 C 1ATPAC5 5 0 12.011 ; qtot > 0 > 11 NR 1ATPAN7 5 -0.3614.0067 ; qtot > -0.36 > 12CR1 1ATPAC8 5 0.36 13.019&# 160; > ; qtot 0 > 13CH1 1ATP AC1* 60.2 13.019 ; qtot > 0.2 > 14 OA 1ATP AO4* 6 -0.3615.9994 ; qtot > -0.16 > 15CH1 1ATP AC4* 6 0.16 13.019 ; qtot > 0 > 16CH1 1ATP AC2* & #160; 7 0.15 13.019 > ; qtot 0.15 > 17 OA 1ATP AO2* 7 -0.54815.9994 ; qtot > -0.398 > 18 H 1ATP AH2* 7 0.398 1.008 ; qtot > 0 > 19CH1 1ATP AC3* 8 0.15 13.019 ; qtot > 0.15 > 20 &# 160; OA 1ATP AO3* 8 -0.54815.9994 > ; qtot -0.398 > 21 H 1ATP AH3* 8 0.398 1.008 ; qtot > 0 > 22CH2 1ATP AC5* 9 0 14.027 ; qtot > 0 > 23 OA 1ATP AO5* 10 -0.36 60; 15.9994 > ; qtot -0.36 > 24 P 1ATPAPA 10 0.70530.9738 ; qtot > 0.345 > 25 OM 1ATP O1PA 10 -0.63515.9994 ; qtot > -0.29 > 26 OM 1ATP O2PA 10 -0.63515.9994 ; qtot > -0.925 > 27 OA 1ATP O3PA &# 160; 11 -0.3615.9994 > ; qtot -1.285 > 28 P 1ATPAPB 11 0.70530.9738 ; qtot > -0.58 > 29 OM 1ATP O1PB 11 -0.63515.9994 ; qtot > -1.215 > 30 OM 1ATP O2PB 11 -0.63515.9994 ; qtot > -1.85 > 31 OA &# 160; 1ATP O3PB 12 -0.3615.9994 > ; qtot -2.21 > 32 P 1ATPAPG 12 0.6330.9738 ; qtot > -1.58 > 33 OM 1ATP O1PG 12 -0.63515.9994 ; qtot > -2.215 > 34 OM 1ATP O2PG 12 -0.63515.9994 ; qtot > -2.85 > ; 35 OA 1ATP O3PG 12 -0.54815.9994 > ; qtot -3.398 > 36 H 1ATP H3PG 12 0.398 1.008 ; qtot > -3 > > [ bonds ] > ; aiaj functc0c1c2c3 > 1 2 2gb_9 > 1 ; 12 2gb_9 > 113 2gb_21 > 2 3 2gb_11 > 210 2gb_15 > 3 4 2gb_6 > 4 5 2gb_6 > 5 6 2gb_11 > 6 7 2gb_8 > 6
[gmx-users] The energy minimization....
http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.htmlMark:I am sorry to disturb you. I'm a beginner of GROMACS and this "mailing-list" system. I even don't know how to replay a post directly. And yesterday I haven't seen your replay because the list title changed, sorry again!About the problem, I haven't resolved it yet. The .top file of my ATP molecule is generated by the pdb2gmx, and the coordinates of each atom adopted to the pdb file. The force file is ffG43a2. Whether my topology file of ATP molecule have something wrong? The topology file of ATP as following:; File '../ATP/ATP.top' was generated; By user: root (0); On host: mjduan-desktop; At date: Wed Aug 15 16:55:53 2007;; This is your topology file; "Does All This Money Really Have To Go To Char ity ?" (Rick);; Include forcefield parameters#include "ffG43a2.itp"[ moleculetype ]; Name nrexclProtein 3[ atoms ]; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NR 1 ATP AN9 1 -0.2 14.0067 ; qtot -0.2 2 C 1 60; ATP AC4 1 0.2 12.011 ; qtot 0 3 NR 1 ATP AN3 2 -0.36 14.0067 ; qtot -0.36 4 CR1 1 ATP AC2 2 0.36 13.019 ; qtot 0 5 NR 1 ATP AN1 3 -0.36 14.0067 ; qtot -0.36 6 C 1 ATP AC6 3 0.36 12.011 ; qtot 0 7 NT 1 ATP AN6 4 -0.83 14.0067 ; qtot -0.83 8 H 1 ATP AH61 4 0.415 1.008 ; qtot -0.415 9 H 1&# 160; ATP AH62 4 0.415 1.008 ; qtot 0 10 C 1 ATP AC5 5 0 12.011 ; qtot 0 11 NR 1 ATP AN7 5 -0.36 14.0067 ; qtot -0.36 12 CR1 1 ATP AC8 5 0.36 13.019&# 160; ; qtot 0 13 CH1 1 ATP AC1* 6 0.2 13.019 ; qtot 0.2 14 OA 1 ATP AO4* 6 -0.36 15.9994 ; qtot -0.16 15 CH1 1 ATP AC4* 6 0.16 13.019 ; qtot 0 16 CH1 1 ATP AC2* & #160; 7 0.15 13.019 ; qtot 0.15 17 OA 1 ATP AO2* 7 -0.548 15.9994 ; qtot -0.398 18 H 1 ATP AH2* 7 0.398 1.008 ; qtot 0 19 CH1 1 ATP AC3* 8 0.15 13.019 ; qtot 0.15 20 &# 160; OA 1 ATP AO3* 8 -0.548 15.9994 ; qtot -0.398 21 H 1 ATP AH3* 8 0.398 1.008 ; qtot 0 22 CH2 1 ATP AC5* 9 0 14.027 ; qtot 0 23 OA 1 ATP AO5* 10 -0.36 60; 15.9994 ; qtot -0.36 24 P 1 ATP APA 10 0.705 30.9738 ; qtot 0.345 25 OM 1 ATP O1PA 10 -0.635 15.9994 ; qtot -0.29 26 OM 1 ATP O2PA 10 -0.635 15.9994 ; qtot -0.925 27 OA 1 ATP O3PA &# 160; 11 -0.36 15.9994 ; qtot -1.285 28 P 1 ATP APB 11 0.705 30.9738 ; qtot -0.58 29 OM 1 ATP O1PB 11 -0.635 15.9994 ; qtot -1.215 30 OM 1 ATP O2PB 11 -0.635 15.9994 ; qtot -1.85 31 OA &# 160; 1 ATP O3PB 12 -0.36 15.9994 ; qtot -2.21 32 P 1 ATP APG 12 0.63 30.9738 ; qtot -1.58 33 OM 1 ATP O1PG 12 -0.635 15.9994 ; qtot -2.215 34 OM 1 ATP O2PG 12 -0.635 15.9994 ; qtot -2.85 ; 35 OA 1 ATP O3PG 12 -0.548 15.9994 ; qtot -3.398 36 H 1 ATP H3PG 12 0.398 1.008 ; qtot -3[ bonds ]; ai aj funct c0 c1 c2 c3 1 2 2 gb_9 1 ; 12 2 gb_9 1 13 2 gb_21 2 3 2 gb_11 2 10 2 gb_15 3 4 2 gb_6 4 5 2 gb_6 5 6 2 gb_11 6 7 2 gb_8 6 10 2 gb_15 7 8 2 gb_2 7 ; 9 2 gb_2 10 11 2 gb_9 11 12 2 gb_9 13 14 2 gb_19 13 16 2 gb_25 14 15 2 gb_19 15 19 2 gb_25 15 22 2 gb_25 16 17 2 gb_19 16 19 2 gb_25 17 18 2 gb_1 19 20 2 gb_19 20 21 2 gb_1 22 23 2 gb_19 23 24 2 gb_27 24 25 2 gb_23 24 26 2 gb_23 24 27 2 gb_27 27 28 2 gb_27 28 29 2 gb_23 28 30 2 gb_23 28 31 2 0; gb_27 31 32 2 gb_27 32 33 2 gb_23 32 34
Re: [gmx-users] The energy minimization....
> Hi, everyone:I have meet some problem when simulating a protein and > ATP complex. The energy minimization will stop after 14 steps. I had > followed Mark's suggestion, did the protein and ATP eneryg minimization > independently, and found that the protein can finish its > minimization correctly, but the ATP 's minimization stopped > after 14 steps. So it seems that there are something wrong with ATP. And > Mark also said "Probably your topology is broken", what is it > means? What should I do now? If you're going to quote somebody from here http://www.gromacs.org/pipermail/gmx-users/2007-August/029115.html, don't imply that they made the comment in relation to another post entirely (unless you're trying to annoy them, that is). I replied to the above question on the list yesterday here http://www.gromacs.org/pipermail/gmx-users/2007-August/029132.html Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The energy minimization....
Hi, everyone:I have meet some problem when simulating a protein and ATP complex. The energy minimization will stop after 14 steps. I had followed Mark's suggestion, did the protein and ATP eneryg minimization independently, and found that the protein can finish its minimization correctly, but the ATP 's minimization stopped after 14 steps. So it seems that there are something wrong with ATP. And Mark also said "Probably your topology is broken", what is it means? What should I do now?Best wishes! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
