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 Özge Kül "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Quoting özge kül : > Thank you Justin A. Lemkul for your interest of my question.I looke

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.Anyo

[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 Özge Kül - Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how._

[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 simulatio

[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 t

[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 lo

[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 -mer

[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. g

[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

[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. g

[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 Cys1–Cys122 disulfide bridge to the B-chain. Most of the A-B chain interactions involve charged side chains; six are buried sal

[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 li

[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

[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 Ha

[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?