Re: [gmx-users] pca-based MD
Hi, Thomas! I'd like to ask you some addition questions about FMA. As I understood from the FMA page that technique is something like integrator of principal components (merge some PCs with identical functional motion seen in the X-ray structures for instance) calculated from g_covar. So FMA is also Hessia-based method (assuming that cov.matrix is inverse of the Hessian) for studing functional motion in protein isnt? Some technical questions: Have you tried to extract functional modes from X-ray data set (not from of unbiased md as in case of EDS) of your kinase for further md-guiding ( e.g by means of EDS) of that protein along some functional modes? Have you tried use it with the gromacs 4.5 ? I've found that only for older gromacs releases. Does it possible to visualise motion along FM in vmd or mol script ? Thanks for help James 2012/9/23 Thomas Evangelidis : > I presume you are referring to Essential Dynamics Sampling, described in > section 3.14 of the manual (v4.5.4). There is also a great tool that finds > the few PCs that are maximally correlated to a functional quantity (e.g. > the volume of the active site). The technique is coined Functional Mode > Analysis (FMA) and you can find more information at: > > http://xray.bmc.uu.se/~jochen/fma.html > > I have used FMA and worked pretty well in my case. I am wondering if anyone > thought of using that technique to find the PCs that are maximally > correlated to a functional quantity and then perform Essential Dynamics > sampling on these PCs to explore the conformational space that affects the > most that functional quantity. > > I.e. I am studying a kinase in the wt and mutant form. Although the > mutation is not near the active site there is a lot of discussion in the > literature about the effect of the mutation on the opening of the catalytic > cleft. Some people claim that one possible explanation of the over-activity > of the mutant is the greater opening of the active site, which facilitates > substrate binding and thus leads to enhanced reaction turn-over. In order > to test this hypothesis with unbiased MD one would need tremendous computer > resources and a lot of time (the kinase is gigantic). On the other hand one > could run short simulations of the wt and mutant, do FMA to find the 10-20 > PCs that are maximally correlated to the volume of the active site, and > then perform Essential Dynamics Sampling on these PCs to explore the > conformational space that is highly correlated to the volume of the active > site. After that, one could safely claim that the Hypothesis was true or > false. > > I would be interested to read your comments on this. > > Thomas > > > On 23 September 2012 11:19, James Starlight wrote: > >> Dear Gromacs Users! >> >> >> There are many publications about implementation of the pca-based MD >> simulations for the investigation of the functional-relevant motions. >> In that cases the eigenvectors are extracted from the relatively short >> MD simulation of the investigated protein and than the biassed MD >> simulation is started along chosen principal component which used as >> the reaction coordinate. >> >> I'd like to know more about implementation of that technique in >> Gromacs. E.g if I've performed some PCA and extracted eigenvectors how >> I can run further simulation along one of the chosen PC ? >> >> Thanks for help >> James >> -- >> 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 >> > > > > -- > > == > > Thomas Evangelidis > > PhD student > University of Athens > Faculty of Pharmacy > Department of Pharmaceutical Chemistry > Panepistimioupoli-Zografou > 157 71 Athens > GREECE > > email: tev...@pharm.uoa.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > -- > 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_L
Re: [gmx-users] Energy minimization
Probably remove the overlapping lipid then. Once you run MD it will repack. On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote: > Thanks for your kind reply. > My system is composed of protein packed by lipids. The atoms overlapping, are > protein ( atom 288) and lipid chain. I think if I move them, I may get some > other clashes, may I not? > Any other suggestion? > > Thanks. > > > > Sincerely, > Shima > > > - Original Message - > From: Peter C. Lai > To: Shima Arasteh ; Discussion list for GROMACS > users > Cc: > Sent: Sunday, December 16, 2012 8:44 AM > Subject: Re: [gmx-users] Energy minimization > > It depends on what the atom is overlapping with and some conjecture as to > what might be causing the overlap: > > You can always manually move it, either by editing the .gro file directly > or using a tool like VMD to move it or the molecule/fragment it's attached to > with the mouse and then display the new coordinates and the update the .gro > file. > If it's something like a solvent molecule (water/lipid) and there is nowhere > to move the molecule, you can try deleting it too (just remmeber to update > .top file). > > On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: > > When I find overlapping atom, what should I have to do? How is it possible > > to get solved? > > > > > > Would you please help me? > > > > > > Sincerely, > > Shima > > > > > > > > From: Justin Lemkul > > To: Shima Arasteh ; Discussion list for > > GROMACS users > > Sent: Saturday, September 29, 2012 3:01 PM > > Subject: Re: [gmx-users] Energy minimization > > > > > > > > On 9/29/12 3:19 AM, Shima Arasteh wrote: > > > > > > Dear all, > > > > > > My system contains lipids, protein and water. > > > I want to energy minimize it, so ran grompp: > > > > > > > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > > > > > and then: > > > # mdrun -v -deffnm em > > > > > > > > > The output is: > > > Steepest Descents: > > > Tolerance (Fmax) = 1.0e+03 > > > Number of steps = 5 > > > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= > > > 518 > > > Stepsize too small, or no change in energy. > > > Converged to machine precision, > > > but not to the requested precision Fmax < 1000 > > > > > > Double precision normally gives you higher accuracy. > > > You might need to increase your constraint accuracy, or turn > > > off constraints alltogether (set constraints = none in mdp file) > > > > > > writing lowest energy coordinates. > > > > > > Back Off! I just backed up em.gro to ./#em.gro.3# > > > > > > Steepest Descents converged to machine precision in 15 steps, > > > but did not reach the requested Fmax < 1000. > > > Potential Energy = 2.3000388e+17 > > > Maximum force = inf on atom 518 > > > Norm of force = inf > > > > > > It seems that atome 518 has an infinite energy. So I tried to apply the > > > suggestion of turning off the constraints in em.mdp. To do so, I added > > > "constraints=none" to mdp file, But it doesn't make different. > > > > > > Any suggestion please? I don't know how to solve this problem. Please > > > help me. > > > > > > > Atom 518 is overlapping with something nearby. You will have to visualize > > the > > system to identify the source of the problem. > > > > -Justin > > > > -- > > > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > gmx-users mailing list gmx-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] Re: Re: Is vacuum simulation NVT?
Dear Dr. Shirts! Could you tell me is there any difference of different Tau_t ussage ( inverse friction in case of Stochastic dynamics) for simulation of water-soluble as well as membrane-proteins ? In the first case I'm using tau_t 2ps that is lower than internal water friction. In the second case one part of protein could be in the membrane ( e.g helixes) but other ( e.g loops) in water media. Both of that solvents have different characteristic viscousity. So what Tau_t should be used in stochastic dynamics for such biphastic systems? James 2012/12/12 Jong Wha Lee : > Thank you very much Justin, and thank you very much Michael. Your replies > were of a great help. > > > > > > Jong Wha > > -- > 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] Essential dynamics (ED) sampling using make_edi
Dear collegues! Oppositely to the Bipin Singh's question I wounder to know about the exploring ( radius expansion) mode of EDS. For example I define essential subspace from some collective coordinates and then run MD in that subspace in exploring mode of EDS. Will the system be biased to the some region of the collective space (like a guided-MD) or its only some steered algorithm of reduction irrelevant degrees of freedom (hight-frequency modes)? What parameters of EDS for time step as well as scope should I use that my simulation be stereed-like not biased-like ? James 2012/12/12 Carsten Kutzner : > Hi Bipin Singh, > > the parameters -deltaF0, -deltaF, -tau, -alpha, and -T are used only > for flooding and have no effect in pure essential dynamics. Which coordinates > appear in the output trajectory (*.trr, *.xtc) is exclusively controlled > by .mdp options (i.e. the group you select there), not by the content of > the .edi file. > > Best, > Carsten > > > On Dec 11, 2012, at 6:27 PM, bipin singh wrote: > >> Hello All, >> >> I want to use the essential dynamics (ED) sampling method to simulate the >> unfolding to folding process using make_edi option of GROMACS. For this >> task I am using -radcon option (acceptance radius contraction along the >> first two eigenvectors towards the folded structure (b4md.gro)) of make_edi >> as below: >> >> *make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro >> -radcon 1-2 -o sam.edi >> * >> *b4md.gro:* folded structure (C-alpha only) >> *topol.tpr: *all atom * >> eigenvec.trr*:from g_covar (C-alpha only) >> >> Is this is the correct way of doing the ED sampling... >> >> >> Also I am not sure about the following: >> >> *1)* How to judge the correct/appropriate value for the: >> >> -maxedsteps >> >> *2)* How to judge the appropriate values for the following parameters for >> an Essential dynamics sampling input *(or it is neglected for ED sampling >> and used only for flooding input ) * >> >> -deltaF0 >> -deltaF >> -tau >> -alpha >> -T >> >> *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain >> all atoms or only the C-alpha atoms (using the above make_edi command). >> >> -- >> *--- >> Thanks and Regards, >> Bipin Singh* >> -- >> 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 > > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > 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] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin, It's not quite understood for me why such errors occurs in the atoms of standard residues when I've bounded them to the C term of my chromophore if the geometry of the adjacent residues might not be changed. So it likely that some errors occur during parametrization of the molecule which I could not identify ( In any case I'll be very thankful for anyone who can provideme with some other version of the integrated chromophore in charm for my future effort-on-errors :) The main problems which I've forced in the improper group definition ( I've not recognize in the paper of simulation in charmm22 what groups should define as improper although Swiss param produce the big set of such groups- see below ) In addition It'll be very hardly to connect chromophore with adjacent residues mainly due to definition of the addition dihedrals. Finally Im not quite sure about CMAP definition ( I've used C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C N 1 24 24\ in the CMAP.itp with the atom names of chromophore C NH1 CT1 C NC=O 1 24 24\ C NC=O CR C=O N=C 1 24 24\ C=C C=O NC=O CR C=O 1 24 24\ C=O NH1 CT1 C NH1 1 24 24\ where NC=O and N=C types correspond to the N and CR is the C-alpha atoms James 2012/12/15, Justin Lemkul : > > > On 12/15/12 2:18 PM, James Starlight wrote: >> So as I understood it've happened because the conformation of the >> adjacent residue is differ when that residue bounded to the >> chromophore ( in comparison to the residue in unbound capped form). > > Conformation is irrelevant; atom types are all that matter here. > >> But in term of the backbone geometry of C and N-terms chromophore is >> like a typical amino acid. Also Chromophore is defined as a protein in >> the residue.dat. When I've examined error log of my system I've >> noticed that missing UB and dihedral parametrs of the i+1 residue have >> never present in the ffbounded.itp ( the exact combination of the >> triplet and quadruplet of atoms for UB and dihedral). Is there any >> other ways to define termi of my non standard residue as the standard >> one? >> > > If a particular bonded interaction is not present in the parent force field, > you > have to derive it parameters for it. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users 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] Energy minimization
Thanks for your kind reply. My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Sunday, December 16, 2012 8:44 AM Subject: Re: [gmx-users] Energy minimization It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: > When I find overlapping atom, what should I have to do? How is it possible to > get solved? > > > Would you please help me? > > > Sincerely, > Shima > > > > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for GROMACS > users > Sent: Saturday, September 29, 2012 3:01 PM > Subject: Re: [gmx-users] Energy minimization > > > > On 9/29/12 3:19 AM, Shima Arasteh wrote: > > > > Dear all, > > > > My system contains lipids, protein and water. > > I want to energy minimize it, so ran grompp: > > > > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > > > and then: > > # mdrun -v -deffnm em > > > > > > The output is: > > Steepest Descents: > > Tolerance (Fmax) = 1.0e+03 > > Number of steps = 5 > > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= > > 518 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up em.gro to ./#em.gro.3# > > > > Steepest Descents converged to machine precision in 15 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = 2.3000388e+17 > > Maximum force = inf on atom 518 > > Norm of force = inf > > > > It seems that atome 518 has an infinite energy. So I tried to apply the > > suggestion of turning off the constraints in em.mdp. To do so, I added > > "constraints=none" to mdp file, But it doesn't make different. > > > > Any suggestion please? I don't know how to solve this problem. Please help > > me. > > > > Atom 518 is overlapping with something nearby. You will have to visualize > the > system to identify the source of the problem. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-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] Energy minimization
It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: > When I find overlapping atom, what should I have to do? How is it possible to > get solved? > > > Would you please help me? > > > Sincerely, > Shima > > > > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for GROMACS > users > Sent: Saturday, September 29, 2012 3:01 PM > Subject: Re: [gmx-users] Energy minimization > > > > On 9/29/12 3:19 AM, Shima Arasteh wrote: > > > > Dear all, > > > > My system contains lipids, protein and water. > > I want to energy minimize it, so ran grompp: > > > > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > > > and then: > > # mdrun -v -deffnm em > > > > > > The output is: > > Steepest Descents: > > Tolerance (Fmax) = 1.0e+03 > > Number of steps = 5 > > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= > > 518 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up em.gro to ./#em.gro.3# > > > > Steepest Descents converged to machine precision in 15 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = 2.3000388e+17 > > Maximum force = inf on atom 518 > > Norm of force = inf > > > > It seems that atome 518 has an infinite energy. So I tried to apply the > > suggestion of turning off the constraints in em.mdp. To do so, I added > > "constraints=none" to mdp file, But it doesn't make different. > > > > Any suggestion please? I don't know how to solve this problem. Please help > > me. > > > > Atom 518 is overlapping with something nearby. You will have to visualize > the > system to identify the source of the problem. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users 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] Energy minimization
When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: > > Dear all, > > My system contains lipids, protein and water. > I want to energy minimize it, so ran grompp: > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > and then: > # mdrun -v -deffnm em > > > The output is: > Steepest Descents: > Tolerance (Fmax) = 1.0e+03 > Number of steps = 5 > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up em.gro to ./#em.gro.3# > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = 2.3000388e+17 > Maximum force = inf on atom 518 > Norm of force = inf > > It seems that atome 518 has an infinite energy. So I tried to apply the > suggestion of turning off the constraints in em.mdp. To do so, I added > "constraints=none" to mdp file, But it doesn't make different. > > Any suggestion please? I don't know how to solve this problem. Please help me. > Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gold-S simulation
Hi fatemeh, I am looking for prameters like yours, where have you took the parameters for gold and gold-aminoacid inteaction? Francesco 2012/12/16 Peter C. Lai > Where is the .itp file for the system? > > On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote: > > hi > > > > > > I'm simulating gold atom interaction with aminoacidcys. I have made > gold-cys.pdb by hyperchem software: > > > > HETATM1 N CYS 1 0.000 1.335 0.000 > > HETATM2 CA CYS 1 -0.683 1.818 -1.183 > > HETATM3 C CYS 1 -0.705 3.339 -1.221 > > HETATM4 O CYS 1 -0.184 3.993 -0.319 > > HETATM5 CB CYS 1 -2.127 1.330 -1.221 > > HETATM6 SG CYS 1 -3.106 1.859 -2.649 > > HETATM8 AU AU 8 -2.833 0.428 -1.793 > > HETATM9 AU AU 9 -2.647 0.381 -2.869 > > HETATM 10 AU AU 10 -1.691 1.360 -3.093 > > HETATM 11 AU AU 11 -0.647 2.706 -2.135 > > HETATM 12 AU AU 12 -2.742 0.834 -0.456 > > HETATM 13 AU AU 13 -1.691 2.061 -0.043 > > HETATM 14 AU AU 14 -0.783 3.136 0.376 > > HETATM 15 AU AU 15 0.095 3.750 -1.068 > > HETATM 16 AU AU 16 -2.929 2.480 -2.204 > > HETATM 17 AU AU 17 -3.285 1.594 -3.328 > > HETATM 18 AU AU 18 -2.544 2.593 -3.763 > > HETATM 19 AU AU 19 -1.951 1.260 -2.303 > > CONECT12 > > CONECT01 > > CONECT2135 > > CONECT02 > > CONECT324 > > CONECT43 > > CONECT526 > > CONECT05 > > CONECT05 > > CONECT65 > > CONECT06 > > CONECT06 > > CONECT06 > > END > > > > > > > > I started simulation by this pdb file. I'm using OPLSAA force field and > also I added gold parameter in ffnonbonded.itp : > > . > > . > > . > > ; Added by DvdS 05/2005 copied from GROMACS force field. > > SI SI 1428.08000 0.000A3.38550e-01 > 2.44704e+00 > > AU AU 79 196.9700 0.000 A0.29510e+00 > 22.1120e+00 > > > > [ nonbond_params ] > > AU AU 10.0e+00 > 0.0e+00 > > > > > > ; SC 08/2007: Special Au-N vdw to simulate chemical bond between > gold-imidazole > > AU opls_511 13.07000e-01 > 3.96000e+00 > > > > ; SC 05/2008: special Au-C and Au-H to simulate pi-systems > alkenes+benzene (and PHE) > > AU opls_142 13.21000e-1 > 2.65400e+00 > > AU opls_143 13.21000e-1 > 2.65400e+00 > > AU opls_144 12.67000e-1 > 1.66500e+00 > > AU opls_145 13.2e-1 > 2.54600e+00 > > AU opls_146 12.67000e-1 > 1.66500e+00 > > AU opls_150 13.21000e-1 > 2.65400e+00 > > > > ; +imidazole and His > > AU opls_506 13.21000e-1 > 2.54000e+00 > > AU opls_507 13.21000e-1 > 2.54000e+00 > > AU opls_508 13.21000e-1 > 2.54000e+00 > > > > ; +HisH > > AU opls_509 13.21000e-1 > 2.54000e+00 > > AU opls_510 13.21000e-1 > 2.54000e+00 > > ; +TYR > > AU opls_166 13.21000e-1 > 2.54000e+00 > > ; +TRP > > AU opls_500 13.21000e-1 > 2.54000e+00 > > AU opls_514 13.21000e-1 > 2.54000e+00 > > AU opls_501 13.21000e-1 > 2.54000e+00 > > AU opls_502 13.55000e-1 > 3.55000e+00 > > > > and I concidered AU-S as bonding connection and I added its parameter > (bond stretch, dihedral and angle ) in ffbonded.itp file: > > [ bondtypes ] > > ; ij func b0 kb > > . > > . > > . > > AUSH 10.24000 165528.0 ; > > AUS 10.24000 165528.0 ; > > AUSG 10.24000 165528.0 ; > > . > > . > > . > > [ angletypes ] > > ; ijk func th0 cth > > . > > . > > . > > AU SG CB 1 109.00 46.34 > > AU SH CB 1 109.00 46.34 > > AU S CB 1 109.00 46.34 > > . > > . > > . > > [ dihedraltypes ] > > . > > . > > . > > #define improper_AU_S_CB_CA-180.0 1.2958 2 > > > > #define improper_AU_SH_CB_CA -180.0 1.2958 2 > > > > #define improper_AU_SG_CB_CA-180 1.2958 2 > > > > #define improper_AU_S_C_C 19 0.9196 2 > > > > #define improper_AU_SH_C_C19 0.9196 2 > > > > #define improper_AU_SG_C_C19 0.9196 2 > > . > > . > > . > > > > when I ru
Re: [gmx-users] gold-S simulation
Where is the .itp file for the system? On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote: > hi > > > I'm simulating gold atom interaction with aminoacidcys. I have made > gold-cys.pdb by hyperchem software: > > HETATM 1 N CYS 1 0.000 1.335 0.000 > HETATM 2 CA CYS 1 -0.683 1.818 -1.183 > HETATM 3 C CYS 1 -0.705 3.339 -1.221 > HETATM 4 O CYS 1 -0.184 3.993 -0.319 > HETATM 5 CB CYS 1 -2.127 1.330 -1.221 > HETATM 6 SG CYS 1 -3.106 1.859 -2.649 > HETATM 8 AU AU 8 -2.833 0.428 -1.793 > HETATM 9 AU AU 9 -2.647 0.381 -2.869 > HETATM 10 AU AU 10 -1.691 1.360 -3.093 > HETATM 11 AU AU 11 -0.647 2.706 -2.135 > HETATM 12 AU AU 12 -2.742 0.834 -0.456 > HETATM 13 AU AU 13 -1.691 2.061 -0.043 > HETATM 14 AU AU 14 -0.783 3.136 0.376 > HETATM 15 AU AU 15 0.095 3.750 -1.068 > HETATM 16 AU AU 16 -2.929 2.480 -2.204 > HETATM 17 AU AU 17 -3.285 1.594 -3.328 > HETATM 18 AU AU 18 -2.544 2.593 -3.763 > HETATM 19 AU AU 19 -1.951 1.260 -2.303 > CONECT 1 2 > CONECT 0 1 > CONECT 2 1 3 5 > CONECT 0 2 > CONECT 3 2 4 > CONECT 4 3 > CONECT 5 2 6 > CONECT 0 5 > CONECT 0 5 > CONECT 6 5 > CONECT 0 6 > CONECT 0 6 > CONECT 0 6 > END > > > > I started simulation by this pdb file. I'm using OPLSAA force field and also > I added gold parameter in ffnonbonded.itp : > . > . > . > ; Added by DvdS 05/2005 copied from GROMACS force field. > SI SI 14 28.08000 0.000 A 3.38550e-01 > 2.44704e+00 > AU AU 79 196.9700 0.000 A 0.29510e+00 22.1120e+00 > > [ nonbond_params ] > AU AU 1 0.0e+00 0.0e+00 > > > ; SC 08/2007: Special Au-N vdw to simulate chemical bond between > gold-imidazole > AU opls_511 1 3.07000e-01 3.96000e+00 > > ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene > (and PHE) > AU opls_142 1 3.21000e-1 2.65400e+00 > AU opls_143 1 3.21000e-1 2.65400e+00 > AU opls_144 1 2.67000e-1 1.66500e+00 > AU opls_145 1 3.2e-1 2.54600e+00 > AU opls_146 1 2.67000e-1 1.66500e+00 > AU opls_150 1 3.21000e-1 2.65400e+00 > > ; +imidazole and His > AU opls_506 1 3.21000e-1 2.54000e+00 > AU opls_507 1 3.21000e-1 2.54000e+00 > AU opls_508 1 3.21000e-1 2.54000e+00 > > ; +HisH > AU opls_509 1 3.21000e-1 2.54000e+00 > AU opls_510 1 3.21000e-1 2.54000e+00 > ; +TYR > AU opls_166 1 3.21000e-1 2.54000e+00 > ; +TRP > AU opls_500 1 3.21000e-1 2.54000e+00 > AU opls_514 1 3.21000e-1 2.54000e+00 > AU opls_501 1 3.21000e-1 2.54000e+00 > AU opls_502 1 3.55000e-1 3.55000e+00 > > and I concidered AU-S as bonding connection and I added its parameter (bond > stretch, dihedral and angle ) in ffbonded.itp file: > [ bondtypes ] > ; i j func b0 kb > . > . > . > AU SH 1 0.24000 165528.0 ; > AU S 1 0.24000 165528.0 ; > AU SG 1 0.24000 165528.0 ; > . > . > . > [ angletypes ] > ; i j k func th0 cth > . > . > . > AU SG CB 1 109.00 46.34 > AU SH CB 1 109.00 46.34 > AU S CB 1 109.00 46.34 > . > . > . > [ dihedraltypes ] > . > . > . > #define improper_AU_S_CB_CA -180.0 1.2958 2 > > #define improper_AU_SH_CB_CA -180.0 1.2958 2 > > #define improper_AU_SG_CB_CA -180 1.2958 2 > > #define improper_AU_S_C_C 19 0.9196 2 > > #define improper_AU_SH_C_C 19 0.9196 2 > > #define improper_AU_SG_C_C 19 0.9196 2 > . > . > . > > when I run my simulation I dont see any interaction or affinity between gold > atom and S atom of cystein, while it is clear that gold shoud has interaction > with sulfur. what is its reason? I'm completely confused. I tried anythings > that I can but my system doesn't work. > > please help me > > > Fatemeh Ramezani > -- > gmx-users mailing listgmx-users@gromacs.org > http
[gmx-users] gold-S simulation
hi I'm simulating gold atom interaction with aminoacidcys. I have made gold-cys.pdb by hyperchem software: HETATM 1 N CYS 1 0.000 1.335 0.000 HETATM 2 CA CYS 1 -0.683 1.818 -1.183 HETATM 3 C CYS 1 -0.705 3.339 -1.221 HETATM 4 O CYS 1 -0.184 3.993 -0.319 HETATM 5 CB CYS 1 -2.127 1.330 -1.221 HETATM 6 SG CYS 1 -3.106 1.859 -2.649 HETATM 8 AU AU 8 -2.833 0.428 -1.793 HETATM 9 AU AU 9 -2.647 0.381 -2.869 HETATM 10 AU AU 10 -1.691 1.360 -3.093 HETATM 11 AU AU 11 -0.647 2.706 -2.135 HETATM 12 AU AU 12 -2.742 0.834 -0.456 HETATM 13 AU AU 13 -1.691 2.061 -0.043 HETATM 14 AU AU 14 -0.783 3.136 0.376 HETATM 15 AU AU 15 0.095 3.750 -1.068 HETATM 16 AU AU 16 -2.929 2.480 -2.204 HETATM 17 AU AU 17 -3.285 1.594 -3.328 HETATM 18 AU AU 18 -2.544 2.593 -3.763 HETATM 19 AU AU 19 -1.951 1.260 -2.303 CONECT 1 2 CONECT 0 1 CONECT 2 1 3 5 CONECT 0 2 CONECT 3 2 4 CONECT 4 3 CONECT 5 2 6 CONECT 0 5 CONECT 0 5 CONECT 6 5 CONECT 0 6 CONECT 0 6 CONECT 0 6 END I started simulation by this pdb file. I'm using OPLSAA force field and also I added gold parameter in ffnonbonded.itp : . . . ; Added by DvdS 05/2005 copied from GROMACS force field. SI SI 14 28.08000 0.000 A 3.38550e-01 2.44704e+00 AU AU 79 196.9700 0.000 A 0.29510e+00 22.1120e+00 [ nonbond_params ] AU AU 1 0.0e+00 0.0e+00 ; SC 08/2007: Special Au-N vdw to simulate chemical bond between gold-imidazole AU opls_511 1 3.07000e-01 3.96000e+00 ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene (and PHE) AU opls_142 1 3.21000e-1 2.65400e+00 AU opls_143 1 3.21000e-1 2.65400e+00 AU opls_144 1 2.67000e-1 1.66500e+00 AU opls_145 1 3.2e-1 2.54600e+00 AU opls_146 1 2.67000e-1 1.66500e+00 AU opls_150 1 3.21000e-1 2.65400e+00 ; +imidazole and His AU opls_506 1 3.21000e-1 2.54000e+00 AU opls_507 1 3.21000e-1 2.54000e+00 AU opls_508 1 3.21000e-1 2.54000e+00 ; +HisH AU opls_509 1 3.21000e-1 2.54000e+00 AU opls_510 1 3.21000e-1 2.54000e+00 ; +TYR AU opls_166 1 3.21000e-1 2.54000e+00 ; +TRP AU opls_500 1 3.21000e-1 2.54000e+00 AU opls_514 1 3.21000e-1 2.54000e+00 AU opls_501 1 3.21000e-1 2.54000e+00 AU opls_502 1 3.55000e-1 3.55000e+00 and I concidered AU-S as bonding connection and I added its parameter (bond stretch, dihedral and angle ) in ffbonded.itp file: [ bondtypes ] ; i j func b0 kb . . . AU SH 1 0.24000 165528.0 ; AU S 1 0.24000 165528.0 ; AU SG 1 0.24000 165528.0 ; . . . [ angletypes ] ; i j k func th0 cth . . . AU SG CB 1 109.00 46.34 AU SH CB 1 109.00 46.34 AU S CB 1 109.00 46.34 . . . [ dihedraltypes ] . . . #define improper_AU_S_CB_CA -180.0 1.2958 2 #define improper_AU_SH_CB_CA -180.0 1.2958 2 #define improper_AU_SG_CB_CA -180 1.2958 2 #define improper_AU_S_C_C 19 0.9196 2 #define improper_AU_SH_C_C 19 0.9196 2 #define improper_AU_SG_C_C 19 0.9196 2 . . . when I run my simulation I dont see any interaction or affinity between gold atom and S atom of cystein, while it is clear that gold shoud has interaction with sulfur. what is its reason? I'm completely confused. I tried anythings that I can but my system doesn't work. please help me Fatemeh Ramezani -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/15/12 2:18 PM, James Starlight wrote: So as I understood it've happened because the conformation of the adjacent residue is differ when that residue bounded to the chromophore ( in comparison to the residue in unbound capped form). Conformation is irrelevant; atom types are all that matter here. But in term of the backbone geometry of C and N-terms chromophore is like a typical amino acid. Also Chromophore is defined as a protein in the residue.dat. When I've examined error log of my system I've noticed that missing UB and dihedral parametrs of the i+1 residue have never present in the ffbounded.itp ( the exact combination of the triplet and quadruplet of atoms for UB and dihedral). Is there any other ways to define termi of my non standard residue as the standard one? If a particular bonded interaction is not present in the parent force field, you have to derive it parameters for it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
So as I understood it've happened because the conformation of the adjacent residue is differ when that residue bounded to the chromophore ( in comparison to the residue in unbound capped form). But in term of the backbone geometry of C and N-terms chromophore is like a typical amino acid. Also Chromophore is defined as a protein in the residue.dat. When I've examined error log of my system I've noticed that missing UB and dihedral parametrs of the i+1 residue have never present in the ffbounded.itp ( the exact combination of the triplet and quadruplet of atoms for UB and dihedral). Is there any other ways to define termi of my non standard residue as the standard one? James 2012/12/15, Justin Lemkul : > > > On 12/15/12 1:34 PM, James Starlight wrote: >> The last problem with which I've forced during preparation of my >> chromophore is when I've defined bond between chromophore and the next >> residue >> >> >> C+N >> >> That produce 15 addition errors about unknown UB and dihedral types >> in the atoms of the next residue (not in the chromophore) where all UB >> and impropers must be defined initially. >> Why that occurs ? >> > > Because the combinations of parameters don't exist in ffbonded.itp. > > -Justin > >> 2012/12/14, James Starlight : >>> The topology with the below params produced that 118 errors during >>> grompp processings ( after pdb2gmx processing the geoetry of the >>> mollecule was correct ) >>> >>> [CRN] >>> [ atoms ] >>> CG2 CA-0.0900 0 >>> CD1 CA-0.0800 1 >>> CD2 CA-0.0800 2 >>> CE1 CA-0.2800 3 >>> CE2 CA-0.2800 4 >>> CZ CA 0.4500 5 >>> NNH1 -0.4700 6 >>> CA1 CPH1 0.1000 7 >>> CB1 CT1 -0.1400 8 >>> CG1 CT30.0900 9 >>> OG1 OH1 -0.6600 10 ;!-0.6800 >>> C1 CPH2 0.5000 11 >>> N2 NR2 -0.6000 12 >>> N3 NR1 -0.5700 13 >>> C2 CPH1 0.5700 14 >>> O3 O -0.5700 15 >>> CA2 CPH1 0.1000 16 >>> CA3 CPH10.1000 17 >>> CC 0.5100 18 >>> OO -0.5100 19 >>> CB2 CE1 -0.1400 20 >>> OH O -0.6200 21 >>> HA1 HB 0.0700 22 >>> HA32 HB 0.0700 23 >>> HA33 HB 0.0700 24 >>> HD1 HP 0.1400 25 >>> HD2 HP 0.1400 26 >>> HE1 HP 0.1000 27 >>> HE2 HP 0.1000 28 >>> HG11 HA 0.0900 29 >>> HG12 HA 0.0900 30 >>> HG13 HA 0.0900 31 >>> HOG1 H 0.4300 32 >>> HB2 HA10.2100 33 >>> H11 H 0.3700 34 >>> HB1 HA10.2100 36 >>> [ bonds ] >>> HG11 CG1 >>> HG12 CG1 >>> CG1 HG13 >>> CG1 CB1 >>> OG1 HOG1 >>> OG1 CB1 >>> CB1 HB1 >>> CB1 CA1 >>> HE2 CE2 >>> NH11 >>> NCA1 >>> CA1 HA1 >>> CA1 C1 >>> CE2 CD2 >>> CE2 CZ >>> HD2 CD2 >>> OH CZ >>> CD2 CG2 >>> CZ CE1 >>> N2 C1 >>> N2 CA2 >>> C1 N3 >>> HA33 CA3 >>> CG2 CB2 >>> CG2 CD1 >>> CE1 HE1 >>> CE1 CD1 >>> CA2 CB2 >>> CA2 C2 >>> N3 CA3 >>> N3 C2 >>> CB2 HB2 >>> CA3 C >>> CA3 HA32 >>> CD1 HD1 >>> C2 O3 >>> CO >>> >>> [ impropers ] >>> CG2 CD1 CB2 CD2 >>> CD1 CE1 CG2 HD1 >>> CD2 CE2 CG2 HD2 >>> CE2 CZ CD2 HE2 >>> CB2 CA2 CG2 HB2 >>> CA2 N2 CB2 C2 >>> C1 CA1 N2 N3 >>> CA1 NC1 CB1 >>> CA1 CB1 C1 HA1 >>> CB1 OG1 CA1 CG1 >>> CB1 CG1 CA1 HB1 >>> C2 N3 CA2 O3 >>> N3 C2 C1 CA3 >>> CA3 CN3 HA33 >>> CA3 HA33 N3 HA32 >>> CZ CE1 CE2 OH >>> CE1 CZ CD1 HE1 >>> CG1 HG11 CB1 HG12 >>> CG1 HG11 CB1 HG13 >>> ; with next residue >>> C+N CA3 O >>> ; with previous residue >>> N-C CA1 H11 >>> [ cmap ] >>> -C N CA1 C1 N2 >>> CA2 C2 N3 CA3 C >>> >>> The only in that I not sure in that model is the corrections in the >>> cmap.itp which I added (I've used first two terms which are correspond >>> to the backbone atoms of the standart amino acid: >>> C NH1 CT1 C NH1 1 24 24\ >>> C NH1 CT1 C N 1 24 24\ >>> and renamed it to the chromophore atom names) >>> >>> by the way If you had had your rtp of the chromophore which you've >>> done in accordance to that paper could you provide me with them for >>> comparison with my model ? >>> >>> >>> James >>> >>> 2012/12/14, Justin Lemkul : On 12/14/12 3:20 PM, James Starlight wrote: > Justin, > > in the case of the system with the atom types assigned from that paper > the grompp produced above 118 errors of non standard bond, angle as > well as dihedral types ;o So it' seems that some 118 addition terms > must be added to the ffbonded.itp to the existing charmm parameters( > it's uncommon for me because in that case the atom names werefrom > standart charmm ff but the total number of errors was bigger than in > case of Swiss params non-standart names usage). > I'm not sure why there were so many errors when you used those parameters. Like I said, we've used them before. I recall a few errors along the way, but manual assignment of the bonded parameters according to the paper is fairly straightforward. > By the way I've simulated choromophore produced by SWISS (
Re: [gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations
On 12/15/12 4:03 AM, mirc...@sjtu.edu.cn wrote: Dear All: I encountered a problem when doing umbrella sampling. The distance calculated by grompp and g_dist is different, as shown by the following: grompp z component of g_dist(since I am constraining the distance between two groups along the z direction, I should calculate the z component of the distance, right?) 2.986 2.96 2.953 2.95 2.931 2.92 2.936 2.9355 2.844 2.83 There is an obvious difference between the distance calculated by the grompp and the g_dist, I also found that some post similar problems in the maillist, but I didn't found answers for the following questions. (1)Why there is a such difference? Probably because the default pull_pbcatom1 doesn't represent your pulled group very well. By default, the atom is chosen as the numerical middle, which may not correspond to the geometric middle in a complex molecule. (2)Also, does anyone know which value is used in the umbrella sampling simulations, the grompp result or the g_dist result? Whatever grompp tells you is what is used. (3)how to choose the right starting conformations since there is such a difference? More likely, you should start by defining pull_pbcatom1 more appropriately. -Justin I also pasted the pull code I used as follows: pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes pull_nstxout= 500 pull_nstfout= 500 pull_ngroups= 1 pull_group0 = Protein pull_group1 = AMA pull_init1 = 0 pull_rate1 = 0.000;nm/ps pull_k1 = 4500 ;kJ/mol/nm^2 Thanks in advance!! Best regards, Ruo-Xu Gu -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Printing thermo data
On 12/15/12 10:58 AM, John Doe wrote: Hello All, I was wondering if it's possible to print to a file different thermo data, such as force on atoms, pressure, bond energies, ect? Energy terms are stored in the .edr file and forces on atoms are stored in the .trr file provided you set nstfout > 0 in the .mdp file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/15/12 1:34 PM, James Starlight wrote: The last problem with which I've forced during preparation of my chromophore is when I've defined bond between chromophore and the next residue C+N That produce 15 addition errors about unknown UB and dihedral types in the atoms of the next residue (not in the chromophore) where all UB and impropers must be defined initially. Why that occurs ? Because the combinations of parameters don't exist in ffbonded.itp. -Justin 2012/12/14, James Starlight : The topology with the below params produced that 118 errors during grompp processings ( after pdb2gmx processing the geoetry of the mollecule was correct ) [CRN] [ atoms ] CG2 CA-0.0900 0 CD1 CA-0.0800 1 CD2 CA-0.0800 2 CE1 CA-0.2800 3 CE2 CA-0.2800 4 CZ CA 0.4500 5 NNH1 -0.4700 6 CA1 CPH1 0.1000 7 CB1 CT1 -0.1400 8 CG1 CT30.0900 9 OG1 OH1 -0.6600 10 ;!-0.6800 C1 CPH2 0.5000 11 N2 NR2 -0.6000 12 N3 NR1 -0.5700 13 C2 CPH1 0.5700 14 O3 O -0.5700 15 CA2 CPH1 0.1000 16 CA3 CPH10.1000 17 CC 0.5100 18 OO -0.5100 19 CB2 CE1 -0.1400 20 OH O -0.6200 21 HA1 HB 0.0700 22 HA32 HB 0.0700 23 HA33 HB 0.0700 24 HD1 HP 0.1400 25 HD2 HP 0.1400 26 HE1 HP 0.1000 27 HE2 HP 0.1000 28 HG11 HA 0.0900 29 HG12 HA 0.0900 30 HG13 HA 0.0900 31 HOG1 H 0.4300 32 HB2 HA10.2100 33 H11 H 0.3700 34 HB1 HA10.2100 36 [ bonds ] HG11 CG1 HG12 CG1 CG1 HG13 CG1 CB1 OG1 HOG1 OG1 CB1 CB1 HB1 CB1 CA1 HE2 CE2 NH11 NCA1 CA1 HA1 CA1 C1 CE2 CD2 CE2 CZ HD2 CD2 OH CZ CD2 CG2 CZ CE1 N2 C1 N2 CA2 C1 N3 HA33 CA3 CG2 CB2 CG2 CD1 CE1 HE1 CE1 CD1 CA2 CB2 CA2 C2 N3 CA3 N3 C2 CB2 HB2 CA3 C CA3 HA32 CD1 HD1 C2 O3 CO [ impropers ] CG2 CD1 CB2 CD2 CD1 CE1 CG2 HD1 CD2 CE2 CG2 HD2 CE2 CZ CD2 HE2 CB2 CA2 CG2 HB2 CA2 N2 CB2 C2 C1 CA1 N2 N3 CA1 NC1 CB1 CA1 CB1 C1 HA1 CB1 OG1 CA1 CG1 CB1 CG1 CA1 HB1 C2 N3 CA2 O3 N3 C2 C1 CA3 CA3 CN3 HA33 CA3 HA33 N3 HA32 CZ CE1 CE2 OH CE1 CZ CD1 HE1 CG1 HG11 CB1 HG12 CG1 HG11 CB1 HG13 ; with next residue C+N CA3 O ; with previous residue N-C CA1 H11 [ cmap ] -C N CA1 C1 N2 CA2 C2 N3 CA3 C The only in that I not sure in that model is the corrections in the cmap.itp which I added (I've used first two terms which are correspond to the backbone atoms of the standart amino acid: C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C N 1 24 24\ and renamed it to the chromophore atom names) by the way If you had had your rtp of the chromophore which you've done in accordance to that paper could you provide me with them for comparison with my model ? James 2012/12/14, Justin Lemkul : On 12/14/12 3:20 PM, James Starlight wrote: Justin, in the case of the system with the atom types assigned from that paper the grompp produced above 118 errors of non standard bond, angle as well as dihedral types ;o So it' seems that some 118 addition terms must be added to the ffbonded.itp to the existing charmm parameters( it's uncommon for me because in that case the atom names werefrom standart charmm ff but the total number of errors was bigger than in case of Swiss params non-standart names usage). I'm not sure why there were so many errors when you used those parameters. Like I said, we've used them before. I recall a few errors along the way, but manual assignment of the bonded parameters according to the paper is fairly straightforward. By the way I've simulated choromophore produced by SWISS ( with the charges assigned from the paper) in the vacuum and didnt notice any inaccuracy in the conformation of chromophore. So the last that I should is the carefull assignment of the 9 missed dihedral terms with the rest of the protein. Sounds like a reasonably approach. Good luck. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please sear
Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/14/12 11:42 PM, James Starlight wrote: The topology with the below params produced that 118 errors during grompp processings ( after pdb2gmx processing the geoetry of the mollecule was correct ) [CRN] [ atoms ] CG2 CA-0.0900 0 CD1 CA-0.0800 1 CD2 CA-0.0800 2 CE1 CA-0.2800 3 CE2 CA-0.2800 4 CZ CA 0.4500 5 NNH1 -0.4700 6 CA1 CPH1 0.1000 7 CB1 CT1 -0.1400 8 CG1 CT30.0900 9 OG1 OH1 -0.6600 10 ;!-0.6800 C1 CPH2 0.5000 11 N2 NR2 -0.6000 12 N3 NR1 -0.5700 13 C2 CPH1 0.5700 14 O3 O -0.5700 15 CA2 CPH1 0.1000 16 CA3 CPH10.1000 17 CC 0.5100 18 OO -0.5100 19 CB2 CE1 -0.1400 20 OH O -0.6200 21 HA1 HB 0.0700 22 HA32 HB 0.0700 23 HA33 HB 0.0700 24 HD1 HP 0.1400 25 HD2 HP 0.1400 26 HE1 HP 0.1000 27 HE2 HP 0.1000 28 HG11 HA 0.0900 29 HG12 HA 0.0900 30 HG13 HA 0.0900 31 HOG1 H 0.4300 32 HB2 HA10.2100 33 H11 H 0.3700 34 HB1 HA10.2100 36 [ bonds ] HG11 CG1 HG12 CG1 CG1 HG13 CG1 CB1 OG1 HOG1 OG1 CB1 CB1 HB1 CB1 CA1 HE2 CE2 NH11 NCA1 CA1 HA1 CA1 C1 CE2 CD2 CE2 CZ HD2 CD2 OH CZ CD2 CG2 CZ CE1 N2 C1 N2 CA2 C1 N3 HA33 CA3 CG2 CB2 CG2 CD1 CE1 HE1 CE1 CD1 CA2 CB2 CA2 C2 N3 CA3 N3 C2 CB2 HB2 CA3 C CA3 HA32 CD1 HD1 C2 O3 CO [ impropers ] CG2 CD1 CB2 CD2 CD1 CE1 CG2 HD1 CD2 CE2 CG2 HD2 CE2 CZ CD2 HE2 CB2 CA2 CG2 HB2 CA2 N2 CB2 C2 C1 CA1 N2 N3 CA1 NC1 CB1 CA1 CB1 C1 HA1 CB1 OG1 CA1 CG1 CB1 CG1 CA1 HB1 C2 N3 CA2 O3 N3 C2 C1 CA3 CA3 CN3 HA33 CA3 HA33 N3 HA32 CZ CE1 CE2 OH CE1 CZ CD1 HE1 CG1 HG11 CB1 HG12 CG1 HG11 CB1 HG13 ; with next residue C+N CA3 O ; with previous residue N-C CA1 H11 [ cmap ] -C N CA1 C1 N2 CA2 C2 N3 CA3 C The only in that I not sure in that model is the corrections in the cmap.itp which I added (I've used first two terms which are correspond to the backbone atoms of the standart amino acid: C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C N 1 24 24\ and renamed it to the chromophore atom names) by the way If you had had your rtp of the chromophore which you've done in accordance to that paper could you provide me with them for comparison with my model ? I gave the files to our collaborators some time ago and archived my own copies. I don't have immediate access to them, sorry. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
The last problem with which I've forced during preparation of my chromophore is when I've defined bond between chromophore and the next residue C+N That produce 15 addition errors about unknown UB and dihedral types in the atoms of the next residue (not in the chromophore) where all UB and impropers must be defined initially. Why that occurs ? James 2012/12/14, James Starlight : > The topology with the below params produced that 118 errors during > grompp processings ( after pdb2gmx processing the geoetry of the > mollecule was correct ) > > [CRN] > [ atoms ] > CG2 CA-0.0900 0 > CD1 CA-0.0800 1 > CD2 CA-0.0800 2 > CE1 CA-0.2800 3 > CE2 CA-0.2800 4 > CZ CA 0.4500 5 > NNH1 -0.4700 6 > CA1 CPH1 0.1000 7 > CB1 CT1 -0.1400 8 > CG1 CT30.0900 9 > OG1 OH1 -0.6600 10 ;!-0.6800 > C1 CPH2 0.5000 11 > N2 NR2 -0.6000 12 > N3 NR1 -0.5700 13 > C2 CPH1 0.5700 14 > O3 O -0.5700 15 > CA2 CPH1 0.1000 16 > CA3 CPH10.1000 17 > CC 0.5100 18 > OO -0.5100 19 > CB2 CE1 -0.1400 20 > OH O -0.6200 21 > HA1 HB 0.0700 22 > HA32 HB 0.0700 23 > HA33 HB 0.0700 24 > HD1 HP 0.1400 25 > HD2 HP 0.1400 26 > HE1 HP 0.1000 27 > HE2 HP 0.1000 28 > HG11 HA 0.0900 29 > HG12 HA 0.0900 30 > HG13 HA 0.0900 31 > HOG1 H 0.4300 32 > HB2 HA10.2100 33 > H11 H 0.3700 34 > HB1 HA10.2100 36 > [ bonds ] > HG11 CG1 > HG12 CG1 > CG1 HG13 > CG1 CB1 > OG1 HOG1 > OG1 CB1 > CB1 HB1 > CB1 CA1 > HE2 CE2 > NH11 > NCA1 > CA1 HA1 > CA1 C1 > CE2 CD2 > CE2 CZ > HD2 CD2 > OH CZ > CD2 CG2 > CZ CE1 > N2 C1 > N2 CA2 > C1 N3 > HA33 CA3 > CG2 CB2 > CG2 CD1 > CE1 HE1 > CE1 CD1 > CA2 CB2 > CA2 C2 > N3 CA3 > N3 C2 > CB2 HB2 > CA3 C > CA3 HA32 > CD1 HD1 > C2 O3 > CO > > [ impropers ] > CG2 CD1 CB2 CD2 > CD1 CE1 CG2 HD1 > CD2 CE2 CG2 HD2 > CE2 CZ CD2 HE2 > CB2 CA2 CG2 HB2 > CA2 N2 CB2 C2 > C1 CA1 N2 N3 > CA1 NC1 CB1 > CA1 CB1 C1 HA1 > CB1 OG1 CA1 CG1 > CB1 CG1 CA1 HB1 > C2 N3 CA2 O3 > N3 C2 C1 CA3 > CA3 CN3 HA33 > CA3 HA33 N3 HA32 > CZ CE1 CE2 OH > CE1 CZ CD1 HE1 > CG1 HG11 CB1 HG12 > CG1 HG11 CB1 HG13 > ; with next residue > C+N CA3 O > ; with previous residue > N-C CA1 H11 > [ cmap ] > -C N CA1 C1 N2 > CA2 C2 N3 CA3 C > > The only in that I not sure in that model is the corrections in the > cmap.itp which I added (I've used first two terms which are correspond > to the backbone atoms of the standart amino acid: > C NH1 CT1 C NH1 1 24 24\ > C NH1 CT1 C N 1 24 24\ > and renamed it to the chromophore atom names) > > by the way If you had had your rtp of the chromophore which you've > done in accordance to that paper could you provide me with them for > comparison with my model ? > > > James > > 2012/12/14, Justin Lemkul : >> >> >> On 12/14/12 3:20 PM, James Starlight wrote: >>> Justin, >>> >>> in the case of the system with the atom types assigned from that paper >>> the grompp produced above 118 errors of non standard bond, angle as >>> well as dihedral types ;o So it' seems that some 118 addition terms >>> must be added to the ffbonded.itp to the existing charmm parameters( >>> it's uncommon for me because in that case the atom names werefrom >>> standart charmm ff but the total number of errors was bigger than in >>> case of Swiss params non-standart names usage). >>> >> >> I'm not sure why there were so many errors when you used those >> parameters. >> Like >> I said, we've used them before. I recall a few errors along the way, but >> manual >> assignment of the bonded parameters according to the paper is fairly >> straightforward. >> >>> By the way I've simulated choromophore produced by SWISS ( with the >>> charges assigned from the paper) in the vacuum and didnt notice any >>> inaccuracy in the conformation of chromophore. So the last that I >>> should is the carefull assignment of the 9 missed dihedral terms with >>> the rest of the protein. >>> >> >> Sounds like a reasonably approach. Good luck. >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the
[gmx-users] Printing thermo data
Hello All, I was wondering if it's possible to print to a file different thermo data, such as force on atoms, pressure, bond energies, ect? Thanks -- 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] different distance calculated by grompp and g_dist when doing umbrella sampling simulations
Dear All: I encountered a problem when doing umbrella sampling. The distance calculated by grompp and g_dist is different, as shown by the following: grompp z component of g_dist(since I am constraining the distance between two groups along the z direction, I should calculate the z component of the distance, right?) 2.986 2.96 2.953 2.95 2.931 2.92 2.936 2.9355 2.844 2.83 There is an obvious difference between the distance calculated by the grompp and the g_dist, I also found that some post similar problems in the maillist, but I didn't found answers for the following questions. (1)Why there is a such difference? (2)Also, does anyone know which value is used in the umbrella sampling simulations, the grompp result or the g_dist result? (3)how to choose the right starting conformations since there is such a difference? I also pasted the pull code I used as follows: pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes pull_nstxout= 500 pull_nstfout= 500 pull_ngroups= 1 pull_group0 = Protein pull_group1 = AMA pull_init1 = 0 pull_rate1 = 0.000;nm/ps pull_k1 = 4500 ;kJ/mol/nm^2 Thanks in advance!! Best regards, Ruo-Xu Gu -- 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
