[gmx-users] (no subject)
Subject: Ion jump out of protein after MD Date: Sat, 14 Mar 2009 09:45:28 +0330 Message-Id: 20090314061153.m77...@razi.tums.ac.ir X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi Sorry I repeat my question again, My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top file in order to prevent this problem. Thanks -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Triclinic water box for a protein MD
You're welcome. Forgot to mention that it comes with an additional .mdp option (rototr = yes/no). That does break compatibility with other versions regarding reading .tpr files. Cheers, Tsjerk On Fri, Mar 13, 2009 at 10:48 PM, TJ Piggot t.pig...@bristol.ac.uk wrote: This looks great thanks, had meant to try and implement something like these restraints for ages but never got round to it, you know how it is ... Tom --On 13 March 2009 21:06 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote: Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an optimally packed system and simulate it with the Gromacs 3.3.1 version you can download from http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz That version of gromacs has the roto-translational constraints implemented that were developed by Andrea Amadei. Mind that the server is fresh :) The paper is about to be submitted. Unfortunately I haven't had time to dig into the GMX 4 code to implement the rotational constraints yet. I wouldn't want to compromise the performance :S Cheers, Tsjerk On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot t.pig...@bristol.ac.uk wrote: You might want to try a rombic dodecahedron box (an option in editconf). Or you can run the simulation using a triclinic box hoping the images don't interact and then check after the simulation has finished using g_mindist -pi on the trajectory, bearing in mind if they do then you will have wasted a lot of time. If you do want to use a triclinic box having a larger amount of water surrounding the complex may be advisable as this makes images interacting less likely Tom --On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, You have to make sure that you're molecule doesn't rotate. Otherwise it will cause direct interactions over the PBC. The same holds true for large conformational changes. Cheers, Tsjerk On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Lucio Montero wrote: I want to simulate a protein complex using a triclinic box, because it reduce my system size in 60%, and consequently the computing time. I have read that using a triclinic box can give problems for a long MD if the peptide has a whirl, but I don´t know if it is a problem for a complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3: 20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of water. I want to run the MD simulating 20 ns. What problems have you read about? Can you cite a source so we know what you're talking about? -Justin Best regards, Lucio Montero -- -- Lucio Ricardo Montero Valenzuela Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM Cuernavaca, Morelos, 62210 - --- ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing list gmx-us...@gromacs.org
[gmx-users] Now there are 16 atoms. Deleted 304 duplicates.
Dear, As a small test, I want to simulate polystyene(PS) using GROMACS. Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating unit(320 atoms totally ) and add the STY residues to the .rtp files. while running pdb2gmx, the procedure was finished successfully. but I find that only 16 atoms are in the generated .gro and .top files. Have you met this strange thing? Or tell me what I should do with it? Best regards, Chaofu Wu xiaowu...@hotmail.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1
Pietro Amodeo wrote: ADDENDUM: I've just compiled Gromacs 3.3.3 on cluster NEW, with Intel compiler (see below). A simulation (still running) on system 2 with the paralled double-prec version shows preliminary results in line with gromacs 3.3.1 on cluster OLD, with no trace of abnormal oscillations and drifts in temperature or energy. Please open a bugzilla and upload the different tpr files. If they indeed crash after short time it should be possible to see what is going on. 2) Cluster: NEW(Infiniband) (CentOS 5) kernel 2.6.18-53.el5 icc 10.1 (Build 20070913 Pack.ID: l_cc_p_10.1.008) fftw 3.2.1 ofed131 - openmpi 1.2.6 Best, Pietro -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Now there are 16 atoms. Deleted 304 duplicates.
xiaowu...@hotmail.com wrote: Dear, As a small test, I want to simulate polystyene(PS) using GROMACS. Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating unit(320 atoms totally ) and add the STY residues to the .rtp files. while running pdb2gmx, the procedure was finished successfully. but I find that only 16 atoms are in the generated .gro and .top files. Have you met this strange thing? Or tell me what I should do with it? The information you are sending here is not complete. How were termini treated, hw was pdb2gmx invoked? How do the building blocks in the rtp file and hdb file look like? Best regards, Chaofu Wu xiaowu...@hotmail.com mailto:xiaowu...@hotmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
Hello. What do you mean by jump? Perhaps the connected MN is a stable state? If you'll supply more details we could try to help you better. --Omer. On Sat, Mar 14, 2009 at 08:15, Homa Azizian haziz...@razi.tums.ac.irwrote: My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top file in order to prevent this problem. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to parametrize Phos. Thr TPO
Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the existing entry for the residue you want to phosphorylate it. here are the notes I made as I did it...comments welcome if anyone doesnt like how I did it! ; TPO which follows is phosphorylated Threonine and was derived thus: ; 1) take THR entry ; 2) add P, O1P, O2P, O3P atoms ; 3) remove HG1 atom ; 4) assign partial charges to give an overall molecule -2 charge ; with this charge localised on the Phosphate group. ; 5) add bonds for OG1 to P and the OxPs. took bond tpyes from [ DADE ] ; 6) likewise took angle types from [ DADE ] ; 7) removed final dihedral which contained H1 (had considered changing it for ; P but dont want to limit Phoshphate group too much) 3) you will need to add the new residue to the file aminoacids.dat if you want the residue to be recognised as part of the protein in subsequent analysis. Make sure you increment the count on the top line of aminoacids.dat. dont put any comments in aminoacids.dat becuase it has unpredictable effects on results. 4) update the hydrogen database entry too if you are expecting pdb2gmx or protonate to work properly. I *think* that was it...! Paul Barrett but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file top_A.itp, line 16530]: No default Proper Dih. types ERROR 0 [file top_A.itp, line 16531]: No default Proper Dih. types Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- Ich Bin Ein Berliner (J.F. Kennedy) * * * * * * Kindly advice nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ion jump out of protein
Hi I mean after MD the ion was not in the active site, the location of ion is out of the protein. My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top file in order to prevent this problem. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using more than one type of molecules
Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ? Sincerely From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, March 13, 2009 8:25:14 PM Subject: Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecules in gromacs. But I'm not sure, so I'm waiting for your contributions. Assume that I have two small organic In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule. Use editconf to set your box size, and genbox -ci -nmol to insert what you need. molecules like hydrocarbons X and Y. I think First I will have to get seperately DRGGMX.ITP and DRGPOH..PDB for the each molecules in different If these come from PRODRG, they will probably require manual modification and validation of their contents. work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water). After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of Y molecule and go on .. Correct. -Justin Could you please help me to learn the true process of using more than one type of molecules in gromacs ? Sincerely ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ion jump out of protein
Homa Azizian wrote: Hi I mean after MD the ion was not in the active site, the location of ion is out of the protein. Then your model physics is wrong and you will have to re-think/re-derive appropriate parameters. -Justin My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top file in order to prevent this problem. -- Tehran University of Medical Sciences www.tums.ac.ir -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to parametrize Phos. Thr TPO
nahren manuel wrote: snip but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file top_A.itp, line 16530]: No default Proper Dih. types ERROR 0 [file top_A.itp, line 16531]: No default Proper Dih. types Then you haven't added all of the proper dihedrals for that particular molecule (phosphates are tricky). There is a parameter set (ffG43a1p) that has a properly-derived set of parameters for phosphorylated amino acids in the User Contributions on the web site. I recall that not all of the formatting was quite right in these files (they were designed for use with Gromacs 3.1.x, IIRC), so if you encounter errors you can contact me off-list and I can send you re-formatted files that I have gotten to work. -Justin Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- Ich Bin Ein Berliner (J.F. Kennedy) * * * * * * Kindly advice nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using more than one type of molecules
Molecular Dynamics wrote: Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some 1. If you are using the original PRODRG, don't. The parameters it generates are for ffgmx, which is deprecated and should not be used. Use PRODRG-2.5 (beta server) and get a Gromos96 43a1-compatible topology. 2. The charges and charge groups assigned by PRODRG are inconsistent, at best. You will need to consult the manual for information about charge groups, and existing elements of the force field to determine whether or not the charges assigned are appropriate. info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y I'm not sure I fully understand. You will obviously have to re-name the files to have them make any sense. You also cannot call both of them DRG within the .pdb and .itp files, as is the output of PRODRG. are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ? Using genbox should be fine. -Justin Sincerely *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, March 13, 2009 8:25:14 PM *Subject:* Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecules in gromacs. But I'm not sure, so I'm waiting for your contributions. Assume that I have two small organic In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule. Use editconf to set your box size, and genbox -ci -nmol to insert what you need. molecules like hydrocarbons X and Y. I think First I will have to get seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in different If these come from PRODRG, they will probably require manual modification and validation of their contents. work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water). After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of Y molecule and go on .. Correct. -Justin Could you please help me to learn the true process of using more than one type of molecules in gromacs ? Sincerely ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list
Re: [gmx-users] using more than one type of molecules
Justin A. Lemkul wrote: Molecular Dynamics wrote: Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some 1. If you are using the original PRODRG, don't. The parameters it generates are for ffgmx, which is deprecated and should not be used. Use PRODRG-2.5 (beta server) and get a Gromos96 43a1-compatible topology. 2. The charges and charge groups assigned by PRODRG are inconsistent, at best. You will need to consult the manual for information about charge groups, and existing elements of the force field to determine whether or not the charges assigned are appropriate. I should also add to this that just because you assign what you believe are reasonable parameters, does not mean they will necessarily be valid. You must validate the parameters appropriately. For Gromos96, this will involve measurements of thermodynamic variables and experimental observables. Refer to the literature regarding the force field. Parameterization is a time-consuming process. While PRODRG does a nice job of automating topology construction, it is the task of the user to actually verify the applicability of the parameters. -Justin info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for example ) . According to your suggestions I will have used DRGGMX.ITP and DRGPOH.PDB files of X molecule, but I will just have used DRGGMX.ITP file of Y molecule. Isn't it important to use DRGPOH.PDB file of Y molecule. Because Y is not a solvent. X and Y I'm not sure I fully understand. You will obviously have to re-name the files to have them make any sense. You also cannot call both of them DRG within the .pdb and .itp files, as is the output of PRODRG. are organic molecules. And I think this is the unique way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could you explain these significant issues ? Using genbox should be fine. -Justin Sincerely *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, March 13, 2009 8:25:14 PM *Subject:* Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more than one type of molecules in gromacs. But I'm not sure, so I'm waiting for your contributions. Assume that I have two small organic In general, the topol.top should consist of the #include statements for each .itp file, then the [ system ] directive should contain a count of each molecule. Use editconf to set your box size, and genbox -ci -nmol to insert what you need. molecules like hydrocarbons X and Y. I think First I will have to get seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in different If these come from PRODRG, they will probably require manual modification and validation of their contents. work directories. Then chose one directory ( X ) and do the operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top If you are using X as the solute and Y as the solvent, then yes, this is fine. It is just like solvating a protein in water (if X = protein, Y = water). After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the number of Y molecule and go on .. Correct. -Justin Could you please help me to learn the true process of using more than one type of molecules in gromacs ? Sincerely ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] how to parametrize Phos. Thr TPO
There is already a user contribution in the gromacs page named ffG43a1p, that is based in the force field ffG43a1 and also includes phosphorilated serine end threonine. However, is exciting doing it for yourself. Mensaje citado por nahren manuel meetnah...@yahoo.com: Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the existing entry for the residue you want to phosphorylate it. here are the notes I made as I did it...comments welcome if anyone doesnt like how I did it! ; TPO which follows is phosphorylated Threonine and was derived thus: ; 1) take THR entry ; 2) add P, O1P, O2P, O3P atoms ; 3) remove HG1 atom ; 4) assign partial charges to give an overall molecule -2 charge ; with this charge localised on the Phosphate group. ; 5) add bonds for OG1 to P and the OxPs. took bond tpyes from [ DADE ] ; 6) likewise took angle types from [ DADE ] ; 7) removed final dihedral which contained H1 (had considered changing it for ; P but dont want to limit Phoshphate group too much) 3) you will need to add the new residue to the file aminoacids.dat if you want the residue to be recognised as part of the protein in subsequent analysis. Make sure you increment the count on the top line of aminoacids.dat. dont put any comments in aminoacids.dat becuase it has unpredictable effects on results. 4) update the hydrogen database entry too if you are expecting pdb2gmx or protonate to work properly. I *think* that was it...! Paul Barrett but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file top_A.itp, line 16530]: No default Proper Dih. types ERROR 0 [file top_A.itp, line 16531]: No default Proper Dih. types Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- Ich Bin Ein Berliner (J.F. Kennedy) * * * * * * Kindly advice nahren Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx error
I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1094904186 while adding improper --- If I comment out CA+N C O improper_O_C_X_Y Then pdb2gmx creates the gro and top with no error messages. I saw an much earlier post by Justin with a similar error message but no resolution. Anyone have anythoughts? Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx error
Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx, VERSION 4.0.3 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1094904186 while adding improper --- If the residue is by itself, something is seriously wrong if pdb2gmx is detecting a billion residues! If I comment out CA+N C O improper_O_C_X_Y Right, because if the residue is by itself, there will be no N in the next residue (+N). Then pdb2gmx creates the gro and top with no error messages. I saw an much earlier post by Justin with a similar error message but no resolution. Anyone have anythoughts? IIRC, that was in reference to version 3.3.1, which turned out to be the result of a broken Ubuntu package, and was not a problem with Gromacs itself. Try it in the context of the actual molecule, if topology construction requires the next residue. In isolation, that residue will always fail with +N. -Justin Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
