[gmx-users] Cys-Cys bonding
Dear Users and masters! I know that gromacs can prepare the topology with covalent bonding of cys-cys bridges in the individual chain on fly. However, when two different chains are connected with such bonds and the intital geometry is satisfactory (distance, angle) It doesn't work. It was done with a charmm36 force field. I used a -ss key and renamed CYS to CYN to be sure that everything was taken into account. Despite the SS atontype marking for SG atoms in topology - nothing have changed.. this bond doesn't exist in MD Thank You in advance! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] secondary structure element constraining
Yes, it does... Should I follow this advices http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ? Phi/Psi lines are like in the sample, with only changed values of atom indexes and angles, measured with pymol of gromacs tools ai ajakal | type | label | phi | dphi kfac power my atom indices | 1 |1 | measured value | 0 1 2 dphi (seems to be 0 if I want to immobilize this geometry) and kfa (is equal to 1 or it means 1000kJmol-1nm-2) as I understood, power label are not implemented and type has only one value = 1. Am I right?? 1. find both phi/psi from the strtucture for each residue 2. add to the top file as You corrected here https://www.researchgate.net/post/How_can_I_change_and_fix_dihedral_angle_during_Gromacs_simulation_using_dihedral_restraints and why are freezing of COM pulling cylinder code (to allow some degree of oscilation) less appropriate methods? or simple genrestr with 1 kJ forces ? Thank You! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] secondary structure element constraining
Yes, it does... Should I follow this advices http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ? Phi/Psi lines are like in the sample, with only changed values of atom indexes and angles, measured with pymol of gromacs tools ai ajakal | type | label | phi | dphi kfac power my atom indices | 1 |1 | measured value | 0 1 2 dphi (seems to be 0 if I want to immobilize this geometry) and kfa (is equal to 1 or it means 1000kJmol-1nm-2) as I understood, power label are not implemented and type has only one value = 1. Am I right?? 1. find both phi/psi from the strtucture for each residue 2. add to the top file as You corrected here https://www.researchgate.net/post/How_can_I_change_and_fix_dihedral_angle_during_Gromacs_simulation_using_dihedral_restraints and why are freezing of COM pulling cylinder code (to allow some degree of oscilation) less appropriate methods? or simple genrestr with 1 kJ forces ? Thank You! On 6/10/18 3:04 AM, alex rayevsky wrote: >* Dear users! *>>* Did anybody meet the problem of positional constraints applied to the *>* secondary structure, namely keeping the 310-helix stable all the time? I've *>* modelled the substructure - a bundle of alpha helices with a 310 helix *>* segment (longer, thinner, reactive) on the one of them. And I need to hold *>* this conformation intact, to study other rearrangements. I'm not sure that *>* freezing is a good way to nail 3-5 residues in a huge system, maybe it is *>* somehow robust. At the same time I tried to simulate the helix with *>* restraints (1 kJ/A^2 XYZ per each atom of the 310 helix part) and the *>* helix moved to the low energy state with a transition '310 -> alpha *>* conformation' without any obstacles. Usually I'm using COM pulling code, *>* but I don't know how to put some constraint on the backbone of these *>* several residues (forming triangle instead of the square, while looking *>* through the helix) without any relation to a surrounding system (without *>* reference atoms), just like a freezing but more realistic, allowing some *>* harmonic oscillations. Any suggestions?? * >It sounds like you want dihedral restraints on your phi and psi torsions. >-Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | (540) 231-3129http://www.thelemkullab.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] secondary structure element constraining
Dear users! Did anybody meet the problem of positional constraints applied to the secondary structure, namely keeping the 310-helix stable all the time? I've modelled the substructure - a bundle of alpha helices with a 310 helix segment (longer, thinner, reactive) on the one of them. And I need to hold this conformation intact, to study other rearrangements. I'm not sure that freezing is a good way to nail 3-5 residues in a huge system, maybe it is somehow robust. At the same time I tried to simulate the helix with restraints (1 kJ/A^2 XYZ per each atom of the 310 helix part) and the helix moved to the low energy state with a transition '310 -> alpha conformation' without any obstacles. Usually I'm using COM pulling code, but I don't know how to put some constraint on the backbone of these several residues (forming triangle instead of the square, while looking through the helix) without any relation to a surrounding system (without reference atoms), just like a freezing but more realistic, allowing some harmonic oscillations. Any suggestions?? Thank You! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Electric field or CompEl protocol?
If I find resources for several calculations (the last one continued for 20 days) I'll try both methods and will share You. It seems I should find another smaller test system and reproduce the approaches. Thank You Sun May 20 09:55:14 CEST 2018 -- I think CompEl is described in the manual, the options for it are here: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html I've never used it, so I can't suggest anything, but you can ask on this board for specific mdp examples. The way CompEl works is conceptually simple: it maintains a transmembrane ionic concentration gradient by swapping ions across the periodic boundary. The result is that on average you get a voltage of (kT/q)log(c_above/c_below) across the system. In reality, you get noisy results (see Fig. 3 (b) in http://www.mpibpc.mpg.de/grubmueller/compel ). On the other hand, if you have long simulated times, you can still get clean data. The problem with using a constant field is that it is only physical for a system with a nearly constant dielectric throughout. I am guessing that is not your case and you have water (epsilon ~80) and a lipid membrane (eps ~ 5?). If there was a real voltage across such a box, it would almost entirely drop across the membrane (i.e. high field across membrane and low field elsewhere). This is why I prefer to use fields that are as low as computationally possible. I would try CompEl at least out of curiosity. In principle, it is a solid idea, but I think this algorithm is clunky and how it agrees with PBC is unclear to me. If you get clean and reasonable data, please let everyone know! :) Alex On 5/20/2018 1:16 AM, alex rayevsky wrote: >* Dear Alex! *>>* Yes, I thought about all Your reflections and I'm also not sure that CompEl *>* is well parameterzied for a non-specialist like me and the electric field *>* is more intuitive for me. However, when I saw the dimension 'V/nm' for the *>* first time, I thought that something must depend on the length of the axis *>*of application (in my case it is about 12 nm) or the thickness of the *>* membrane. *>* These two of 20 articles I've found on the theme befor wrote in gmx *>* society: *>* Structural and Functional Effect of an Oscillating Electric Field on the *>* Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI: *>* 10.1371/journal.pone.0166412 ) and Molecular dynamics of ion transport *>* through the open conformation of a bacterial voltage-gated sodium channel. *>* ( https://doi.org/10.1073/pnas.1214667110 <https://doi.org/10.1073/pnas.1214667110>). ANd this method works fine, in *>* general, they've got what they wanted. *>* But there is no full description of parameterization. what can You say? *>>* Thank You *>>>* At the same time compel method is very popular too, here is another mention *>* of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016 <http://dx.doi.org/10.1016/j.bpj.2017.02.016> *>>>* Alex <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=from:%22Alex%22 <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=from:%22Alex%22>> *>* Sat, 19 May 2018 17:35:15 -0700 *>* <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=date:20180519 <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=date:20180519>> *>>* It's more of a philosophical question in, unfortunately. I don't use *>* CompEl, because I believe it is conceptually clunky, but that's a *>* matter of opinion that could turn into discussion beyond the scope of *>* your question. I don't study biomolecules, so I can get away with *>* applying direct fields. For biomolecules, however, I do suggest at *>* least looking into CompEl and how it works, and then choosing *>* appropriate setup sothat you do not slow down your simulation too *>* much. *>>* That said, 0.4 V/nm does not really correspond to 40 mV in any way. The best *>* "fake" guess is that the voltage drop across the entire box is its height, *>* times the value of E-z. It is fake, because your field has nothing to do *>* with the solution of the Poisson's equation, or the box height. The *>* consequences of this field do, but the field itself doesn't, if that makes *>* sense. One other point to be made: water's dielectric breakdown threshold *>* is around 100 MV/m = 0.1 V/nm. Noone in the community that publishes in *>* Biophysical Journal seems to care about it, but huge simulated fields can *>* be incompatible with what's being studied. *>>* My response probably doesn't help much, but this is the situation with all *>* MD software that relies on Ewald summation. *>>* Alex *>>>* On 5/19/2018 5:16 PM, alex rayevsky wrote: *>>* Dea
Re: [gmx-users] Electric field or CompEl protocol?
Dear Alex! Yes, I thought about all Your reflections and I'm also not sure that CompEl is well parameterzied for a non-specialist like me and the electric field is more intuitive for me. However, when I saw the dimension 'V/nm' for the first time, I thought that something must depend on the length of the axis of application (in my case it is about 12 nm) or the thickness of the membrane. These two of 20 articles I've found on the theme befor wrote in gmx society: Structural and Functional Effect of an Oscillating Electric Field on the Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI: 10.1371/journal.pone.0166412 ) and Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel. ( https://doi.org/10.1073/pnas.1214667110). ANd this method works fine, in general, they've got what they wanted. But there is no full description of parameterization. what can You say? Thank You At the same time compel method is very popular too, here is another mention of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016 Alex <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=from:%22Alex%22> Sat, 19 May 2018 17:35:15 -0700 <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=date:20180519> It's more of a philosophical question in, unfortunately. I don't use CompEl, because I believe it is conceptually clunky, but that's a matter of opinion that could turn into discussion beyond the scope of your question. I don't study biomolecules, so I can get away with applying direct fields. For biomolecules, however, I do suggest at least looking into CompEl and how it works, and then choosing appropriate setup sothat you do not slow down your simulation too much. That said, 0.4 V/nm does not really correspond to 40 mV in any way. The best "fake" guess is that the voltage drop across the entire box is its height, times the value of E-z. It is fake, because your field has nothing to do with the solution of the Poisson's equation, or the box height. The consequences of this field do, but the field itself doesn't, if that makes sense. One other point to be made: water's dielectric breakdown threshold is around 100 MV/m = 0.1 V/nm. Noone in the community that publishes in Biophysical Journal seems to care about it, but huge simulated fields can be incompatible with what's being studied. My response probably doesn't help much, but this is the situation with all MD software that relies on Ewald summation. Alex On 5/19/2018 5:16 PM, alex rayevsky wrote: Dear all, Which protocol, Electric field section or the CompEl, I should use in the situtation: 1. I built an ion channel by homology, prepared a bilayer membrane, embeded my protein and run a simulation to relax the system (100 ns) 2. my channel was closed all the time. 3. I want to run four parallel simmulations, starting from the relaxed state: a) system under the effect of -80 mV and under +40 mV - the second one should cause a pore opening; b) both previous variants with a ligand in the pore; The voltage sensitive domain of the Nav channel should respond to the electric stimuli, that is why I thought it is reasonable to apply it to Z direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for example. other parameters should stay intact, I think, because I don't know if they should be changed... at the same time I've read several different works when CompEl was implemented to the membrane-channel systems. The end of the pagehttp://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs manual, however I didn't find any mention of a voltage handling and what exactly I'll obtain at the end Which method is more approrpiate for my task? Thank You !! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Electric field or CompEl protocol?
Dear all, Which protocol, Electric field section or the CompEl, I should use in the situtation: 1. I built an ion channel by homology, prepared a bilayer membrane, embeded my protein and run a simulation to relax the system (100 ns) 2. my channel was closed all the time. 3. I want to run four parallel simmulations, starting from the relaxed state: a) system under the effect of -80 mV and under +40 mV - the second one should cause a pore opening; b) both previous variants with a ligand in the pore; The voltage sensitive domain of the Nav channel should respond to the electric stimuli, that is why I thought it is reasonable to apply it to Z direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for example. other parameters should stay intact, I think, because I don't know if they should be changed... at the same time I've read several different works when CompEl was implemented to the membrane-channel systems. The end of the page http://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs manual, however I didn't find any mention of a voltage handling and what exactly I'll obtain at the end Which method is more approrpiate for my task? Thank You !! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start it with a voltage of +40 mV. As I understoond it should be distributed along Z-axis but I don't know how to deal with correspondent three values in mdp in the elecric field section and how to assign a side with a higher or lower potential (to choose a correct direction for ion permeability). It seems that it should look like this: """ ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = ' E-xt = 'not implemented' E-y = E-yt = 'not implemented' E-z = 1 4 0 or 1 -8 0 E-zt = 'not implemented' """ the first : only 1 is implemented (with frequency 0) so enter 1, the second : the strength of the electric field in V nm-1, the third : any number here since a cosine of frequency zero has no phase. """ The reason for such manipulation is investigation of inhibitory conditions affecting the opening of the pore...I didn't find any tutors on the theme. Of course, I could start the md and then tune the mdp file, but the system is about a half of a million atoms and it will take too much time. Thank You! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ion channel in lipid bilayer
Dear Peter, thank You for responce! I've already prepared toplogy file, here is a content: ; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "/home/dikov/alex/WORK/lipid/charmm36.itp" #include "LIG.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_A2.itp" #include "topol_Other_chain_A3.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_B2.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_C2.itp" #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_D2.itp" ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include POPG chain topology #include "POPG.itp" ; Include water topology #include "/home/dikov/alex/WORK/lipid/TIP3.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm36-jul2017.ff/ions.itp" #include "POT.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A21 Other_chain_A3 1 Protein_chain_B 1 Protein_chain_B21 Protein_chain_C 1 Protein_chain_C21 Protein_chain_D 1 Protein_chain_D21 LIG 1 POT 118 POPG96 ''' Insane script is for Martini, am I right? Charmm-gui was very confusing and hard to generate orientation. However, if no ohter suggestions available, I'll try Your's! Thank You!! >>>> ___ Kroon, P.C. Sun, 18 Feb 2018 15:52:30 -0800 <https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=date:20180218> Hi Alex, Try either insane.py, or charmm-gui. I can't provide links, since I'm on my phone. You may need to generate the topology (itp) of the protein, which you can do with calling pdb2gmx on just the protein. You should have a topology (itp) of your favourite lipid. Peter 2018-02-17 0:56 GMT+02:00 alex rayevsky <rayevsk...@gmail.com>: > Hi all! > > I have a question concerning immersion of the ion channel (four subunits > with extracellular domains and a bundles of helixes) into the lipid > bilayer. 6 years ago I used some tutorial or mailing lists, which described > the way from KALP15 tutor. With CCR5 model there were no problems at all. > Now I have a not 'cylindric' protein with a complex shape and overhanging > domains. > the forcefield is CHARMM36, lipid type - POPG. > > I tried Membrane builder, but couldn't orient the plane of the membrane by > changing XYZ principles many times in different combinations.. Thus I used > a slightly modified KALP15 method (other .itps, lipids and water > molecules). First of all after pdb2gmx for protein a series of > topologies were generated with identifiers in the name, as it was assigned > in each chain. However editconf produced a new pdb from the outpu gro > without any ID or terminators for the chains, in Pymol it is represented > with a tetramer entirely highlithing if a single chain is selected (maybe > it is a reason of faults at later stages). > > Well, it works fine until the perl script execution. Beside some problems > with the output (system_inflated.gro was corrupted, but I repaired it with > simple python scripting and got a pretty protein in the center of rare > molecules, which looks reliable enough) I started to compact the bilayer to > rich the lipid area of ~53A^2. I finished it on the 13 stage of perl > execution - the distance between nearest lipids was about 16A, however, the > layer was really holey. At the same time the protein was not surrounded > from all sides. But if I try to put lipids closely one to other, they are > simultaneously penetrate the protein body. > > Is it the correct method for such kind of simmulations? Could I increase > the number of POPG molecules after getting inflated.gro file with scaled up > bilayer (the initial step for tightning) before scaling iterations? I can > do it manually by copy of the layer (all lipid coordinates) and its > rotation around Y axis in any soft to enlarge the number of molecules in > the cell (even 200 mols is more than 128). Of course I will make changes in > a topology file. It seems, that I will obtain a fully wrapped protein > without anxiety about clashes or presure in cavities... > > What do You think? Thank You in advance! > > > > *Nemo me impune lacessit* > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: ion channel in lipid bilayer
I'm sorry for repeat, but nobody answered the question and I decided to duplicate the request. Maybe it is a problem with a form of question or its content, please, point me the mistake. Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains and a bundles of helixes) into the lipid bilayer. 6 years ago I used some tutorial or mailing lists, which described the way from KALP15 tutor. With CCR5 model there were no problems at all. Now I have a not 'cylindric' protein with a complex shape and overhanging domains. the forcefield is CHARMM36, lipid type - POPG. I tried Membrane builder, but couldn't orient the plane of the membrane by changing XYZ principles many times in different combinations.. Thus I used a slightly modified KALP15 method (other .itps, lipids and water molecules). First of all after pdb2gmx for protein a series of topologies were generated with identifiers in the name, as it was assigned in each chain. However editconf produced a new pdb from the outpu gro without any ID or terminators for the chains, in Pymol it is represented with a tetramer entirely highlithing if a single chain is selected (maybe it is a reason of faults at later stages). Well, it works fine until the perl script execution. Beside some problems with the output (system_inflated.gro was corrupted, but I repaired it with simple python scripting and got a pretty protein in the center of rare molecules, which looks reliable enough) I started to compact the bilayer to rich the lipid area of ~53A^2. I finished it on the 13 stage of perl execution - the distance between nearest lipids was about 16A, however, the layer was really holey. At the same time the protein was not surrounded from all sides. But if I try to put lipids closely one to other, they are simultaneously penetrate the protein body. Is it the correct method for such kind of simmulations? Could I increase the number of POPG molecules after getting inflated.gro file with scaled up bilayer (the initial step for tightning) before scaling iterations? I can do it manually by copy of the layer (all lipid coordinates) and its rotation around Y axis in any soft to enlarge the number of molecules in the cell (even 200 mols is more than 128). Of course I will make changes in a topology file. It seems, that I will obtain a fully wrapped protein without anxiety about clashes or presure in cavities... What do You think? Thank You in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ion channel in lipid bilayer
Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains and a bundles of helixes) into the lipid bilayer. 6 years ago I used some tutorial or mailing lists, which described the way from KALP15 tutor. With CCR5 model there were no problems at all. Now I have a not 'cylindric' protein with a complex shape and overhanging domains. the forcefield is CHARMM36, lipid type - POPG. I tried Membrane builder, but couldn't orient the plane of the membrane by changing XYZ principles many times in different combinations.. Thus I used a slightly modified KALP15 method (other .itps, lipids and water molecules). First of all after pdb2gmx for protein a series of topologies were generated with identifiers in the name, as it was assigned in each chain. However editconf produced a new pdb from the outpu gro without any ID or terminators for the chains, in Pymol it is represented with a tetramer entirely highlithing if a single chain is selected (maybe it is a reason of faults at later stages). Well, it works fine until the perl script execution. Beside some problems with the output (system_inflated.gro was corrupted, but I repaired it with simple python scripting and got a pretty protein in the center of rare molecules, which looks reliable enough) I started to compact the bilayer to rich the lipid area of ~53A^2. I finished it on the 13 stage of perl execution - the distance between nearest lipids was about 16A, however, the layer was really holey. At the same time the protein was not surrounded from all sides. But if I try to put lipids closely one to other, they are simultaneously penetrate the protein body. Is it the correct method for such kind of simmulations? Could I increase the number of POPG molecules after getting inflated.gro file with scaled up bilayer (the initial step for tightning) before scaling iterations? I can do it manually by copy of the layer (all lipid coordinates) and its rotation around Y axis in any soft to enlarge the number of molecules in the cell (even 200 mols is more than 128). Of course I will make changes in a topology file. It seems, that I will obtain a fully wrapped protein without anxiety about clashes or presure in cavities... What do You think? Thank You in advance! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear users and developers! I have a question about replica exchange sampling and simulation annealing method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11 residues, which are probably exposured to the solvent (and it seems are flexible enough to be invisible for X-ray). The protein exists in two isoforms, which differ on a single amino acid (approximately -15 position from the end), however, some in-house biochemical experiments stated that this change is crucial for motility of these terminal 10-15 residue. The problem is that I can't predict the exact initial location/conformation of the full-length C-termini and all standard MD simulations showed different, not similar, positions of the region - it can be either flexible or pinned to the 'protein's body' during the MD. It seems, that it depends on the seed which turns on a trigger for rotation of exposured straight 10-15 res. C-termini... Before starting a production MD for subsequent analysis I should be somehow ensured that the initial conformation is reliable. i-Tasser is not a good way, because it doesn't guarantee nothing, except the total minimization state, and homology modelling is also impotent. That is why I want to start a preliminary MD to sample these C-terminal end (rebuild with any program like pymol, molsoft or swissmodel server) and I bet on these two approaches, mentioned above. Does anybody know is it possible, reasonable? where I can find a working tutorial to provide some changes or use it as it is? The additional question is about 'partial application' of the method to the fragment of the protein, to avoid time consuming calculations for the whole system, which is not a priority, as the final goal is just a minimized protein with a more informed preparation alghorithm. Thank You in advance!!! *Nemo me impune lacessit* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
