Re: [gmx-users] rtp file
Hi Justin A. Lemkul , Thank you for your answer.Your answer made me clear suddenly.:)And I think I found the rigth way :) Thank you Ãzge Kül "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting özge kül : > Thank you Justin A. Lemkul for your interest of my question.I looked at my > 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with > that fatal error.I thougth that my pdb structure had wrong structure and then > I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an > idea? The program ends in a fatal error because there is in fact no atom called LPD1 within a methionine residue, as far as the force field (and most standard nomenclature) is concerned. Read the error message: "atom LPD1 not found." If LPD1 is a lone pair, as you claim, than it is obviously not an atom, and hence why pdb2gmx is complaining. Is this residue something you modified in Sybyl? Because I can't find anything in 4htc.pdb that says LPD1. -Justin > > Thank you very much > Ãzge Kül > Hacettepe University > Chemistry Department > "Justin A. Lemkul" wrote: > Quoting özge kül : > > > Hi all, > > > > I try to use gromacs for my callculations of thrombin structure.I obtained > > the pdb from protein databank.But the structure has some missing residues > at > > the end of the chain and et the beginning of the chain.I completed the > > residues with sybyl 7.3.And then I started to my simulation.But in the > > pdb2gmx command I got this > > > > fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms. > > That means the residue has atoms that are named differently than those in the > .rtp file. If the atom does indeed belong, determine what it is and rename it > in the .pdb file, not the .rtp. > > > > > Then I looked at the .rtp file.I want to learn how can I add a missing > > thing to the .rtp file.I search for the list that have the same titile.But > > one of you please write me how can I do this.My simulation is depend on > this > > fatal error. > > You should not make changes to the .rtp file unless you absolutely know what > you're doing. > > -Justin > > > > > Thank you very much > > Ãzge Kül > > > > Hacettepe University > > Chemistry Department > > > > > > - > > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it > > now. > > > > > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > - > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it > now. Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rtp file
Thank you Justin A. Lemkul for your interest of my question.I looked at my 4htc.pdb file but I saw that LPD1 MET11.I don't understand why it ends with that fatal error.I thougth that my pdb structure had wrong structure and then I looked it up in the sybyl program.I saw LPD1 lone pair there.Anyone has an idea? Thank you very much Ãzge Kül Hacettepe University Chemistry Department "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting özge kül : > Hi all, > > I try to use gromacs for my callculations of thrombin structure.I obtained > the pdb from protein databank.But the structure has some missing residues at > the end of the chain and et the beginning of the chain.I completed the > residues with sybyl 7.3.And then I started to my simulation.But in the > pdb2gmx command I got this > > fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms. That means the residue has atoms that are named differently than those in the .rtp file. If the atom does indeed belong, determine what it is and rename it in the .pdb file, not the .rtp. > > Then I looked at the .rtp file.I want to learn how can I add a missing > thing to the .rtp file.I search for the list that have the same titile.But > one of you please write me how can I do this.My simulation is depend on this > fatal error. You should not make changes to the .rtp file unless you absolutely know what you're doing. -Justin > > Thank you very much > Ãzge Kül > > Hacettepe University > Chemistry Department > > > - > Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it > now. Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rtp
Hi all, I want to ask also how can I exit from the .rtp file?If I made some changes in the .rtp file ,how can I exit? Thank you very much Ãzge Kül - Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rtp file
Hi all, I try to use gromacs for my callculations of thrombin structure.I obtained the pdb from protein databank.But the structure has some missing residues at the end of the chain and et the beginning of the chain.I completed the residues with sybyl 7.3.And then I started to my simulation.But in the pdb2gmx command I got this fatal error.:Atom LPD1 in MET11 not found in rtp entry with 9 atoms. Then I looked at the .rtp file.I want to learn how can I add a missing thing to the .rtp file.I search for the list that have the same titile.But one of you please write me how can I do this.My simulation is depend on this fatal error. Thank you very much Ãzge Kül Hacettepe University Chemistry Department - Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fatal error
Hi Amanda , I got the same error with you.I have tried to calculate a protein structure which has two chains.This chains are bound with eachother with disulphide bonds.I used -merge -ignh -ss in pdb2gmx.Have you solved your problem .This the error message: Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 4 out of 8 --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. If you got some decision about this problem,please help me.I looked up all the message in the list,but Icouldn't find. Thank U - Ahhh...imagining that irresistible "new car" smell? Check outnew cars at Yahoo! Autos.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] lambda
Hi everybody, I try to calculate a protein which has two chains.This chains has sulphide bridges between eachother.I used -merge in pdb2gmx.I calculated for 20ns.I said free energy:no. But I got this error: Fatal error: > Too many LINCS warnings (10716) - aborting to avoid logfile runaway. > This normally happens when your system is not sufficiently > equilibrated,or if yo > u are changing lambda too fast in free energy simulations. > If you know what you are doing you can adjust the lincs warning threshold > in your mdp file, but normally it is better to fix the problem. > I looked at mailing list.Idecided to change delta-lambda=0.2 Can anyone help me about this? Thank you - Ahhh...imagining that irresistible "new car" smell? Check outnew cars at Yahoo! Autos.___ gmx-users mailing list[EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting chains
Hi My question was about my molecule has two chains and I at least (after several analyze graphics)understood the chains are splitting up and then get together when I watched the protein in VMD.The chains get together with SS bonds.I read the manual then I got the information about -merge.And I only want to ask do you know anything else except -merge ? Thank you - TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting chains
Hi Eric, Where is the specbond.dat?After which line is it formed? 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr Please help me?:) özge - Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting chains
Hi Andrea, This is my .top file more 1ppbfree.top ; ; File '1ppbfree.top' was generated ; By user: ozge (502) ; On host: druggrid ; At date: Thu Mar 15 23:17:25 2007 ; ; This is your topology file ; ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W ; ; Include forcefield parameters #include "ffG43a1.itp" ; Include chain topologies #include "1ppbfree_H.itp" #include "1ppbfree_L.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W in water [ molecules ] ; Compound#mols Protein_H 1 Protein_L 1 SOL 8695 Thank you very much again and again... - No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting chains
Hi Eric, Where is the specbond.dat?After which line is it formed? 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr Please help me?:) özge - Get your own web address. Have a HUGE year through Yahoo! Small Business.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spliting chains
Hi, Thank you for your advices.The A-chain is topologically similar to the activation peptide of chymotrypsin(ogen) and connected in a similar manner through the Cys1ÂCys122 disulfide bridge to the B-chain. Most of the A-B chain interactions involve charged side chains; six are buried salt bridges, and 10 are involved in interchain hydrogen bonds .In VMD I saw the two chains split up at atime and then get together.I only know that I should write -merge in pdb2gmx line.According to the informations above how can you help me? 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr - Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting of chains
After making Md simulation and getting the rmsd,gyration.. analyzing graphics I looked at the VMD.Then I saw that the 2 chains are getting splitting at a time.And then got together.So I could understand why the graphics are so bad.Then I read the manual.It says I should use -merge in pdb2gmx line if you have disulphite bridges.My molecule has 2 chains that has disulfite bonds..Anything else that you know about this except -merge? Thank you özge - Don't pick lemons. See all the new 2007 cars at Yahoo! Autos.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] two chains
Hi Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain?Are the parameters must be different ?Also I want to ask about trajconv.Where I had to add the pbc?I want to send you my directions. 1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr or is the pbc used in the script? Thank You very much Ãzge - It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] my big problem
Hi everybody, I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error : Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 7 additional processes aborted (not shown) I only can think about the difference may be caused because of my protein -ligand complex is very big.It has 2 chains. After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy, nstxtcoutvalues than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics.Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files? thank you .. - Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gen_vel
HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes? THANK YOU... - Don't pick lemons. See all the new 2007 cars at Yahoo! Autos.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
