[gmx-users] Freezing group
Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use a R.E.D.III server. As there are several different fitting methods, so I have to carry out a series of short MDs (about 5-10 ns) for each of them. The question is - is it possible to isolate this domain and fix/freeze last residues of the hairpin/linker to prevent movement of domain segments? I know that this is not the way to study ligand-protein interaction, however I just want to use it for understanding which topology generation method is better. Thank you! -- * Nemo me impune lacessit* -- 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] Implicit solvent
Hi, dear developers! I want to ask you abou dynamics in implicit solvent. I have a complex of animal protein - dimer/trimer. After modeling by homology I have built another one from the plant organism. Dimer/trimer was constructed with superposition method. The question is - can I use imlicit solvent model to optimize and relax this complex? Is it real and where I can find suitable parameters of mdp? Thank you -- * Nemo me impune lacessit* -- 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] repost_hybrid imlicit/explicit solvent
Hi this is a repost, maybe it was missed. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein molecule with ligand in the binding site and than fill the box with continuous imlicit solvent with epsilon = 80. To prevent the departure of discrete water molecules into the implicit layer I want to limit the distance of their movement with something like PULL COM distance or anything else. Is it real or I have to find another way or choose another software for this purpose. Thank you in advance -- * Nemo me impune lacessit* -- 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] hybrid solvent model
Hi all. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein molecule with ligand in the binding site and than fill the box with continuous imlicit solvent with epsilon = 80. To prevent the departure of discrete water molecules into the implicit layer I want to limit the distance of their movement with something like PULL COM distance or anything else. Is it real or I have to find another way or choose another software for this purpose. Thank you in advance -- * Nemo me impune lacessit* -- 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] Phosphorylation
Hi, all. Does anybody know wether I have to put a phosphorylated residue in the kinase's activation loop (last example is pdbid 2Y94) or not, when I'm working with protein-inhibitor complex without any type of protein-protein interactions? Or it is necessary only when I'm working with p-p complexes? The maximum time of dynamics is 10 ns. Any suggestions or links will be appreciated! Thank you for reply! -- Nemo me impune lacessit -- 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] amber-lipid
Hi Is it possible to use amber forcefield with lipid parameters like it was done with gmx in KALP-15 in DPPC tutorial? I have to use amber forcefield as it is neccessary for parametrization of my ligand and its stecking interactions. Thank you very much -- Nemo me impune lacessit -- 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] several itp
Hi all. Justin, thank you for you quick respons ))) I want to clarify a situation with a number of ligands I can use in one simulation. I have got files of 3 ligands converted from amber files to gromacs with amb2gmx.pl script. To include this files in the topology file I changed the extension of this files from top to itp. Is it possible to include several .itp files in the section: ; Include forcefield parameters #include ***.ff/forcefield.itp #include lig1.itp #include lig2.itp #include In this case I've got an error with order of inputs... Or I can add this topologies as top files in the section [ molecules ]...? Thank you -- * Nemo me impune lacessit* -- 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] pull_distance
hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pulling distance Y Y Y for it with pull_k1 = 2000 and pull_init1 = with pull_rate1 = 0? Will it hold the initial distance all the time and how many groups I have to create? Will it be enough 2 groups (one with a selected atoms from first chain and another with atoms from the second) in the index file or I have to create sveral groups which will consist of a pairs of groups of atoms involved in h-bonding? As I understood in this way I will handle a center of mass, so the first variant is preferable. Is it true? Thank you for responce -- * Nemo me impune lacessit* -- 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] ATP+Mg
Hi all. I need your advices about my task which is closely associated with ATP toplogy in the binding site. As I understood from one of the letters ( http://archive.ambermd.org/201106/0522.html) I can use antechamber or derive charges from the site linked in the letter. But the ATP's phosphate tail is very flexible and very negatevly charged thus I need too coordinate it with Mg ion to prevent an increased flexibility and motion. Here are some of my questions: 1. What parts of initial structure I have to prepare and process with antechamber - separate adenylate and metal or both of them together like a compound? 2. After getting separate topologys / complex topology - is it necessary to constrain the distances between PO2 groups and metal to be sure this tail won't move anyway during MD or this coordination bond is strong enough? Thank you -- * Nemo me impune lacessit* -- 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] MD duration
Hi all. I want to ask you a question about the length of dynamics. Is it enough to set time at 3-5ns to see the motion and affinity of the ligand (nucleotide derivate) the protein's domain size is nearly 200 aminoacids. The protein was optimized earlier. Moreover, is it enough for drug design screening to compare such derivatives? Thank you! -- * Nemo me impune lacessit* -- 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] cyclosporine A
Hi! I need an advice concerninng topology building of such substance like cyclosporine A. I've tried to make it with antechamber tool, cause I wanted to use amber99sb forcefield. But the program gave me an error in the begining and no results in the end after 12 hours of calculations ))) Can you give any suggestions for my next steps? This compound is a peptide chain built from acyl-adenylated amino acids (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid, 4-methylthreonine, and D-alanine). Thank you very much! -- * Nemo me impune lacessit* -- 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] Re: gmx-users Digest, Vol 90, Issue 82
No I need your help in any way, antechamber is not only the way I could do it, I think...I just showed you that I tried something before I wrote you a letter. It is not necessary to use amber forcefield, but I don't think that prodrg is a good choice for this task, though the only modification of the residues in the peptide is acylation. But may be you know something! Thank you very much? On 17/10/2011 5:01 PM, Алексей Раевский wrote: Hi! I need an advice concerninng topology building of such substance like cyclosporine A. I've tried to make it with antechamber tool, cause I wanted to use amber99sb forcefield. But the program gave me an error in the begining and no results in the end after 12 hours of calculations ))) Can you give any suggestions for my next steps? This compound is a peptide chain built from acyl-adenylated amino acids (L-valine, L-leucine, L-alanine, L-glycine, 2-aminobutyric acid, 4-methylthreonine, and D-alanine). Thank you very much! If you're asking for antechamber help, you're on the wrong forum. Mark -- 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] angke definition
Hi, i need your help again! this time in the selection of analyzing tools and methods... I've found a water molecule near one of the ligand atoms. It's stabile enough and the distance is about 3.3 A. But I want to make some measurments, exactly angle degree identification. I want to calculate the frequence of forming of angle (about 90 degree) between oxygen of the water and the plane (formed by the atom of the ligand and several atoms around (it is a first CA atom and carboxyl group CA-C-O-OH of aminoacid)). But a perpendicular from OW is connected exactly to C atom of carboxyl group. In other case gromacs is trying to calculate an angle between OW and the whole, unlimited plane... Can I do such analyze? Ormay be you can give me some advices Thank you! -- * Nemo me impune lacessit* -- 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] Re: gmx-users Digest, Vol 89, Issue 52
mm...sorry for incorrect explanation of the task. I know how to use index_ndx and g_select, but I don't know whether it is possible to create an index group of all atoms in !!sphere!! with a radius of 10 angstrom around selected carbon (for example). Exactly I don't know how and where to determine a sphere's parameters. As you understand if this sphere includes SOL molecules (which are flexible and all time will be changing one to another from outside to the inside of the sphere), so I have to define not atom numbers of SOL but constant spatial character of the sphere. IS IT possible? With a use of index file it will look like a new index.ndx, with [sphere] section and its content, for each frame -- Message: 4 Date: Sat, 10 Sep 2011 00:00:23 +0300 From: ??? rayevsk...@gmail.com Subject: [gmx-users] (no subject) To: gmx-users@gromacs.org Message-ID: CAB6CZ-=eZHExKyUJRBXrxpAAa0zkHxT=apgyae_jh6bne7y...@mail.gmail.com Content-Type: text/plain; charset=koi8-r Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you -- *ó Í! *** * Nemo me impune lacessit* -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110910/3611a8e9/attachment-0001.html -- Message: 5 Date: Fri, 09 Sep 2011 17:02:40 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e6a7ef0.9050...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed Алексей Раевский wrote: Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you Use g_select to generate the index group and trjconv to write the file in the format (and with the contents) that you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- *С уважением! *** * Nemo me impune lacessit* -- 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] (no subject)
Hi. I've look through the manual and didn't find an answer on my question: i've got a trajectory and i want to convert it in *.pdb with such parameters of index file [all atoms within a sphere with a chosen radius around selected atom]. What can i do? Thank you -- *С уважением! *** * Nemo me impune lacessit* -- 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] mdp params and forcefields
Hi. I need your help dealing with parametrization of mdp file. Look, I want to understand how can we change such params like rlist, rvdw, cut-off, rcoulomb. As I know each forcefield has its own properties and calculated values of this params. But I've found that in different articles this values were the same, though the forcefields were not... Also I've read that each meaning of this params I can change depeding on my task... Changing rlist we will get more accurate results, as there are more atoms around the one, which motion is calculated, will be considered. And what about other params? What for, as example, we can cut-off an influence of coulumb forces with reducing the distance of them? In what situation I can change them and how it will affect the result? And also were can I find some defined parameters of mdp for charmm27 or amber99, I mean not from articles, but any supplements which come with forcefield files... THANK YOU VERY MUCH -- *С уважением! *** * Nemo me impune lacessit* -- 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] Re: gmx-users Digest, Vol 83, Issue 130
Hi! I'm working with kinase with ATP in active site. ATP topology was created by swissparam.ch http://swissparam.ch server, as well as I'm working with charmm27 in gromacs 4.5.3. Using superposition of the protein models I've found coordinates for ions which have to stabilize ATP (Mg2+). For this purpose we used MgCl in the real experiments. I know, that Zn atoms in protein I can bind changing protonation type of aminoacid CYS and HIS which formed 4 bonds with Zn. And I need your help in this question! Of course I shouldn't create bond and angel between etheric O and magnesium. May be I have to PULL this Mg2+ atoms? and if it is so - which PULLING method I need (distance or else)? I don't see how pulling is relevant here. You could use it to enforce a restraint, but it's not necessary. Distance restraints or type 6 bonds are probably more useful and straightforward. You do certainly have the complication of whether or not the force field's charges for the amino acids are correct, which most likely they aren't, as most QM/MM studies would indicate. -Justin Thank you very much Thank you for a reply ))) First of all I've understood that Pulling is a bad idea. I tried to apply several manuals, including this one http://www.gromacs.org/Documentation/How-tos/Distance_Restraints. But what about typing of 6 bonds? Bonds between ATP and Mg, Mg aminoacids? This part of your message is unclear whether or not the force field's charges for the amino acids are correct, which most likely they aren't what aa did you mean, those I described with Zn binding or supposed Mg binding? Sorry for I repeat the question -- 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] ATP+Mg
Hi! I'm working with kinase with ATP in active site. ATP topology was created by swissparam.ch server, as well as I'm working with charmm27 in gromacs 4.5.3. Using superposition of the protein models I've found coordinates for ions which have to stabilize ATP (Mg2+). For this purpose we used MgCl in the real experiments. I know, that Zn atoms in protein I can bind changing protonation type of aminoacid CYS and HIS which formed 4 bonds with Zn. And I need your help in this question! Of course I shouldn't create bond and angel between etheric O and magnesium. May be I have to PULL this Mg2+ atoms? and if it is so - which PULLING method I need (distance or else)? Thank you very much -- 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] (no subject)
Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the binding site. Something like a coordination molecule. So a command g_dist with index file and distance 0.35 showed me a number of water molecule I needed. But when I decided to visualize this process I saw that my protein with rna went out from the water box to another cell and the part of rna sppeared in the bottom of this box (( as I know this is not a bug or error of pbc. But i don't understand what is happening. Does my water forms bonds with this part and aminoacids (!!!) of binding site, because when I've converted trr to pdb with index file (atoms of binding site, part of rna, water molecules I've got with g_dist) I saw water molecules with part of rna in the bottom of display and binding site in the top...I tried to use -pbc nojump and center, -pbc mol...this flags united protein, rna and part of rna togetrher, but my water is not there Thank you -- 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] include a few .itp files
Hi. I have some problems using ff_charmm27 ported in gromacs 4.5.3. 1) I want to build a topology of phosphorylated tyrosine in one position of activated protein. I can make it with swissparam.ch server (getting .itp) or by my hands. But the situation is complicated enough for me, because of necessity to add some hydrogenes (to ester O in phosphate group) to the structure from Marvel Sketch. In other case server claimed the mol2 file is bad. So what to do? Add hydrogens to this oxygenes or not? I'm not sure it is right... I think they must be 'free' from H... 2) I need to include several .itp (tyrosine-PO3 and ligand). Adding strings include... before [molecule] section in the top of .top file. And when I did grompp i've got an error invalid order [atomtype] for the last itp. It isn't important which .itp is first, cause the exchange of the strings order do nothing: just an error for the 'new' last .itp Thank you -- 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] Reducing distance between atoms! PULL
Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology ...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constrained MD simulation was performed to investigate the mechanisms of the approach of the water molecule. This simulation was started by using a harmonic potential as the distance constraint, where the force constant was set to 5 kcal/mol å2. When the atomic distance was not reduced any further, despite the presence of the harmonic potential in the MD simulation (at about 470 ps), the force constant was increased up to 200 kcal/mol å2; this was exploited to mimic the first phase of a nucleophilic attack..all together about 1ns and The atomic distance is 3.4 A, suggesting that this water molecule acts as a nucleophile in the post-transfer editing reaction.. I have to reduce distance between oxygen of H2O and carbon during simulation, but H2O must be free enough for revolution around C. Index file is ready for it. This is part of mdp. ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 1 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = C pull_weights0 = pull_pbcatom0 = 0 pull_group1 = H2O pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 1.0 pull_init1 = 3.4 pull_rate1 = 0.02 pull_k1 = 837 pull_kB1 = 837 Is everything ok with pull_vec1, pull_init1, pull_rate1 (if I put 0 atoms will stay without any movement, but I suggest it will cause another result), pull (umbrella is harmonical, constrains - no) and pull_geometry (in the article was mentioned distance instead of direction) ??? I did experiments with different changes in parameters...Waiting for your comments. 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/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/mailing_lists/users.php
[gmx-users] Pulling water
Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology ...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constrained MD simulation was performed to investigate the mechanisms of the approach of the water molecule. This simulation was started by using a harmonic potential as the distance constraint, where the force constant was set to 5 kcal/mol Е2. When the atomic distance was not reduced any further, despite the presence of the harmonic potential in the MD simulation (at about 470 ps), the force constant was increased up to 200 kcal/mol Е2; this was exploited to mimic the first phase of a nucleophilic attack..all together about 1ns and The atomic distance is 3.4 A, suggesting that this water molecule acts as a nucleophile in the post-transfer editing reaction.. I have to reduce distance between oxygen of H2O and carbon during simulation, but H2O must be free enough for revolution around C. Index file is ready for it. This is part of mdp. ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 1 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = C pull_weights0 = pull_pbcatom0 = 0 pull_group1 = H2O pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 1.0 pull_init1 = 3.4 pull_rate1 = 0.02 pull_k1 = 837 pull_kB1 = 837 Is everything ok with pull_vec1, pull_init1, pull_rate1 (if I put 0 atoms will stay without any movement, but I suggest it will cause another result), pull (umbrella is harmonical, constrains - no) and pull_geometry (in the article was mentioned distance instead of direction) ??? I did experiments with different changes in parameters...Waiting for your comments. 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/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/mailing_lists/users.php
[gmx-users] COM Pulling
Hi all ! I have a results of my MD and i have found a water molecule that was getting closer to my substrate on one frame of my dynamic. The distance is 3.4 A. Now I have to immobillize this water on this distance during the next step of MD by using a harmonic potential as the distance constraint, where the force constant is about 200 kcal/I understand that i have to create an index file, it's ok, but my mdp is bad rather COM pulling in gromacs 4.0.5... protein - my substrate LIN - my water ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = Protein pull_weights0 = pull_pbcatom0 = 0 pull_group1 = LIN pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 0.0 pull_init1 = 0.34 pull_rate1 = 0.0 pull_k1 = 837 pull_kB1 = 837 I've also tried cylynder geometry, changing pull_dim = ... but my water still goes out. Thank you for help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 2 questions
Hi all. I'm working with gromacs 4.0.5 in amber99 force field. I have two questions: 1. The protein part of my complex (trna+protein) consists of 870 aminoacids and two atoms of Zn. The question is - whether I have to create an index file, which will unit aminoacids and Zn in one protein or not? If not - whether those Zn will be stable during dynamics or they will escape from the structure in the water? 2. One of the goals of my work is studing of aminoacyl-adenylat behavior: look, when I added aminoacid to adenyn through O2' in hyperchem and then created topology everything was fine untill I get to dynamics (even steep and gradient)... results I saw were very bad, aminoacid flied away from adenyn...I thought gromacs doesn't see this bond between aminoacid and nucleotide...saw I created a new topology for it! It represents both elements (aa and nucleotide) as a one. And I have written a new bond in ff...bon.itp . This is examples of my work - fragments of a) .rtp, b) .hdb, c) ff..bon.itp: a)[ RA3 ] [ atoms ] N amber99_39 0.05770 1 H9 amber99_24 0.22720 2 CA amber99_11 -0.00540 3 HA amber99_28 0.10930 4 CB amber99_11 0.31960 5 HB amber99_18 -0.02210 6 CG1 amber99_11 -0.31290 7 HG11 amber99_18 0.07350 8 HG12 amber99_18 0.07350 9 HG13 amber99_18 0.07350 10 CG2 amber99_11 -0.31290 11 HG21 amber99_18 0.07350 12 HG22 amber99_18 0.07350 13 HG23 amber99_18 0.07350 14 C amber99_2 0.61630 15 O amber99_41 -0.57220 16 P amber99_46 1.16620 17 O1P amber99_45 -0.77600 18 O2P amber99_45 -0.77600 19 O5' amber99_44 -0.49890 20 C5' amber99_11 0.05580 21 H5'1 amber99_19 0.06790 22 H5'2 amber99_19 0.06790 23 C4' amber99_11 0.10650 24 H4' amber99_19 0.11740 25 O4' amber99_44 -0.35480 26 C1' amber99_11 0.03940 27 H1' amber99_20 0.20070 28 N9 amber99_40 -0.02510 29 C8 amber99_6 0.20060 30 H8 amber99_24 0.15530 31 N7 amber99_36 -0.60730 32 C5 amber99_4 0.05150 33 C6 amber99_3 0.70090 34 N6 amber99_38 -0.90190 35 H61 amber99_17 0.41150 36 H62 amber99_17 0.41150 37 N1 amber99_37 -0.76150 38 C2 amber99_9 0.58750 39 N3 amber99_37 -0.69970 40 C4 amber99_4 0.30530 41 C3' amber99_11 0.20220 42 H3' amber99_19 0.06150 43 C2' amber99_11 0.06700 44 H2'1 amber99_19 0.09720 45 O2' amber99_44 -0.61390 46 HO'2 amber99_25 0.41860 47 O3' amber99_43 -0.65410 48 H1 amber99_17 0.22720 49 H2 amber99_17 0.22720 50 H3 amber99_17 0.22720 51 [ bonds ] P O1P P O2P P O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' C4' O4' C4' C3' O4' C1' C1' H1' C1' N9 C1' C2' N9 C8 N9 C4 C8 H8 C8 N7 N7 C5 C5 C6 C5 C4 C6 N6 C6 N1 N6 H61 N6 H62 N1 C2 C2 H9 C2 N3 N3 C4 C3' H3' C3' C2' C3' O3' C2' H2'1 C2' O2' O3' HO'2 O2' C -O3' P N H1 N H2 N H3 N CA CA HA CA CB CA C CB HB CB CG1 CB CG2 CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 CG2 HG22 CG2 HG23 C O C +N [ dihedrals ] O4' C1' N9 C4 proper_X_CT_N*_X C1' N9 C8 H8 proper_X_CK_N*_X C1' N9 C8 N7 proper_X_CK_N*_X C1' N9 C4 C5 proper_X_CB_N*_X C1' N9 C4 N3 proper_X_CB_N*_X H1' C1' N9 C8 proper_X_CT_N*_X H1' C1' N9 C4 proper_X_CT_N*_X C8 N9 C4 C5 proper_X_CB_N*_X C8 N9 C4 N3 proper_X_CB_N*_X C5 C6 N1 C2 proper_X_CA_NC_X N6 C6 N1 C2 proper_X_CA_NC_X N1 C2 N3 C4 proper_X_CQ_NC_X H9 C2 N3 C4 proper_X_CQ_NC_X H8 C8 N7 C5 proper_X_CK_NB_X N9 C8 N7 C5 proper_X_CK_NB_X H62 N6 C6 N1 proper_X_CA_N2_X H61 N6 C6 N1 proper_X_CA_N2_X C5 C6 N6 H61 proper_X_CA_N2_X C5 C6 N6 H62 proper_X_CA_N2_X H8 C8 N9 C4 proper_X_CK_N*_X N7 C8 N9 C4 proper_X_CK_N*_X O5' C5' C4' H4' proper_H_CT_CT_O H5'1 C5' C4' O4' proper_H_CT_CT_O H5'2 C5' C4' O4' proper_H_CT_CT_O O4' C4' C3' H3' proper_H_CT_CT_O O4' C1' C2' H2'1 proper_H_CT_CT_O C2' O2' C CA proper_H_CT_CT_O CA C +N +H backbone_prop_1 O C +N +H backbone_prop_2 CA C +N +CA backbone_prop_1 O C +N +CA backbone_prop_1 [ impropers ] C4 C8 N9 C1' nucleic_imp_10 C6 H61 N6 H62 N9 N7 C8 H8 N1 N3 C2 H9 nucleic_imp_11 C5 N6 C6 N1 nucleic_imp_11 CA +N C O b)RA3 14 2 6 H5' C5' O5' C4' 1 5 H4' C4' C5' O4' C3' 1 5 H1' C1' O4' N9 C2' 1 1 H8 C8 N9 N7 2 3 H6 N6 C6 C5 1 1 H9 C2 N1 N3 1 5 H3' C3' C4' C2' O3' 1 5 H2'1 C2' C1' C3' O2' 1 2 HO'2 O3' C3' C4' 3 4 H N CA CB 1 5 HA CA N CB C 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA c)CT OS C 1 109.500 502.080 ; (amber99_11 12.01000 ; CT sp3 aliphatic C/ amber99_44 16.0 ; OS ether and ester oxygen/ amber99_2 12.01000 ; C sp2 C carbonyl group/) The problem is that, when I tried molecule of aminoacyladenylate in dynamics - everything is ok. But in complex there a lot of warnings and errors with pdb2gmx topology creating. First of all, when I did my first efforts I described above (when I added aminoacid to adenyn through O2' in hyperchem and then created topology everything was fine untill I get to dynamics) I had atom name O2 in RC and RU (cytozine, uracyl) in pdb file and had no problems, but now gromacs couldn't find it, and I saw that in .rtp it has name O...ok, I changed all O2 in cytozynes and
[gmx-users] PULLING
Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know how to create index group (like protein or non-protein), cause I have to unite H2O (the most close to the carbonyl carbon) and the carbonyl carbon of valyn, just an atom not full residue. So I don't understand how to identify this atom for gromacs...by number of atom in whole structure or something else? P.S. about the list of functions in mdp I sent you, I wanted to be sure I have chosen everything I had to...according to the article... Thank you very much, sory for disturb. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PULLING
Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know how to create index group (like protein or non-protein), cause I have to unite H2O (the most close to the carbonyl carbon) and the carbonyl carbon of valyn, just an atom not full residue. So I don't understand how to identify this atom for gromacs...by number of atom in whole structure or something else? P.S. about the list of functions in mdp I sent you, I wanted to be sure I have chosen everything I had to...according to the article... Thank you very much, sory for disturb. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 67, Issue 89
Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know how to create index group (like protein or non-protein), cause I have to unite H2O (the most close to the carbonyl carbon) and the carbonyl carbon of valyn, just an atom not full residue. So I don't understand how to identify this atom for gromacs...by number of atom in whole structure or something else? P.S. about the list of functions in mdp I sent you, I wanted to be sure I have chosen everything I had to...according to the article... Thank you very much, sory for disturb. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PULLING
Hi all. I have to reproduce an experiment from the article Identification of the nucleophilic factors and the productive complex for the editing reaction by leucyl-tRNA synthetase (by Yohsuke Hagiwara a,b, Osamu Nureki c, Masaru Tateno a,b,*). This is one of the steps of education I have to complete. All actions described in this article were made with Amber9. I'm a newer in modelling and I have only gromacs tools (v4.0.4), so I have downloaded amber force field port-files (E.J. Sorin, S. Park). I want to know whether my mdp files are reflexing the data I need. So this is a chapter from article: ...1. MD simulations were performed using the AMBER 9 program. The parm99 force field was applied to the atoms of LeuRS and tRNALeu, and the TIP3P model was used for the solvent water molecules. Electrostatic interactions were calculated by the particle-mesh Ewald (PME) method, using 1.0 as the dielectric constant. A cut-off of 12 Е was used to calculate the direct space sum for PME; the electrostatic interactions beyond 12 Е were calculated in reciprocal space by the fast Fourier transform method. Thus, all electrostatic interactions between atoms were calculated. The SHAKE algorithm was used to restrain the bond lengths involving hydrogen atoms. The time step for integration was set to 1 fs. The temperature and pres-sure were set using the Berendsen algorithm. The initial coordinates used for the present MD simulations were from the modelled structure previously constructed for LeuRS complexed with valyl-tRNALeu. For the present system, we immersed the complex in a solvent box comprising 49 587 water molecules, and used the periodic boundary condition where the size of the unit box was 103.0 _ 138.3 _ 117.1 Е3. The total number of atoms in the system was 165 739. In the initial (relaxation) phase of the MD simulation, the water molecules were relaxed at 300 K for 10 ps, while the atoms of the protein and tRNALeu were positionally constrained by a harmonic function using a force constant of 500 kcal/mol Е2. The force constant was then reduced to 250, 125, 50, 25, 10, and 5 kcal/mol Е2 in six MD simulations. The time consumed by each simulation was 2 ps...(then free MD)... 2. This equilibrated system was used for further structural modeling to investigate the hydrated structure relevant to the editing reaction, in which 1 ns MD simulations were performed in the presence of constraints to effectively explore the states. First, with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constrained MD simulation was performed to investigate the mechanisms of the approach of the water molecule. This simulation was started by using a harmonic potential as the distance constraint, where the force constant was set to 5 kcal/mol Е2. When the atomic distance was not reduced any further, despite the presence of the harmonic potential in the MD simulation (at about 470 ps), the force constant was increased up to 200 kcal/mol Е2; this was exploited to mimic the first phase of a nucleophilic attack in the MD simulations, which enabled us to explore larger conformational spaces than with the first principles MD simulations. A similar protocol was applied in other constrained MD simulations for efficient explorations of conformational spaces. To obtain a PMF with respect to the rotation of the dihedral angle, C40-C30-O30-HO30 , we employed the umbrella sampling technique, using 14 windows in the range of 50-180_. Umbrella sampling is a theoretical technique to efficiently search for not only energetically favourable but also energetically-unfavourable conformations in a phase space of a system, combined with a bias potential (e.g. a harmonic potential) to overcome energy barriers. The force constants of the potential in those windows were set to 10.0 kcal/mol rad2. The structures obtained using MD simulations were evaluated by exploiting quantum mechanics/molecular mechanics (QM/MM) hybrid calculations in terms of the stability and reactivity. For this purpose, our interface program was used to connect QM (gamess) andMM(amber) engines... Questions: 1.First of all, can I use spc instead op tip3p? Some problems occured when I tried to full the genbox with water... not enough memory (it's not true, I made my box corresponding to the values mentioned above). 2. First part of MD (1.) cpp = /lib/cpp -traditional ; define = -DFLEXIBLE; constraints = hbonds constraint_algorithm = SHAKE integrator = md dt = 0.001 nsteps = 2 nstxout = 2000 nstxtcout = 2000 nstvout = 2000 nstfout = 2000 nstlog = 2000 coulombtype = PME rcoulomb= 1.0 rcoulomb_switch = 0 pme_order = 4 optimize_fft= yes fourierspacing = 0.12 ns_type
