Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

Check the program Biomer. I allows you to create any type of DNA molecule: http://casegroup.rutgers.edu/Biomer/index.html You will also need the amber forcefield for DNA. Gerrit Message: 7 Date: Fri, 10 Apr 2009 12:21:33 +0800 From: li ming Subject: Re: [gmx-users] How to obtain a appro

[gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of two domains and perform

Re: [gmx-users] Pressure Coupling Problem

Nope not an A/nm problem. As a simple test I take spc.gro from share/top. I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o water_center. I then solvate with genbox, minimize and run using the mdp file I provided earlier. No matter how much minimization I do the volume of the

Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

Hi, Mark: I want to check the chain length of DNA on the translocation time through a nanopore. So the DNA chains with different polymerization but the same monomer structure is necessary. How can I solve this problem? Does anybody has a optimized DNA pdb file for GMX simulation? Thanks a lot!!

Re: [gmx-users] visualize atom number backbone

shahrbanoo karbalaee wrote: Dear justin I want compare two rmsf atoms from two peptide(backbone).then I need have atom in backbone. there is the column lable atoms .but in spdbv ,atom numbering for backbone is simillar peptide (backbone+side chain).would you please tell me for visuallize atom nu

Re: [gmx-users] How to obtain a approperiate PDB file of DNA?

li ming wrote: Hi, all... I have a question on the pdb files of DNA: How can I obtain an appropriate DNA pdb file for GMX simulation? I just download some pdb files from Internet, but it is not compatible for GMX, saying that the residue was not found in rtp file. How can I solve this prob

[gmx-users] visualize atom number backbone

Dear justin I want compare two rmsf atoms from two peptide(backbone).then I need have atom in backbone. there is the column lable atoms .but in spdbv ,atom numbering for backbone is simillar peptide (backbone+side chain).would you please tell me for visuallize atom numbering backbon ,what do I do?

[gmx-users] How to obtain a approperiate PDB file of DNA?

Hi, all... I have a question on the pdb files of DNA: How can I obtain an appropriate DNA pdb file for GMX simulation? I just download some pdb files from Internet, but it is not compatible for GMX, saying that the residue was not found in rtp file. How can I solve this problem? Are the reference

[gmx-users] Thank you

Dear Justin; Thank you very much, your answers solved my questions, but ocurred new errors which will resolve to further. I go try new parameters create for PVC's atoms now. Thank you Jessé da Nóbrega Graduating in pharmacy from the Federal University of Paraíba - Brazil Veja quais são

[gmx-users] Pressure Coupling Problem

So your problem with the small water box was solved simply by adding more minimization? I then suspect that all of your problems are simply related to a bad starting structure -- and by the sound of it is really is very bad. Are you sure that you don't have an angstrom / nm problem here? Chris

Re: [gmx-users] Re: gmx-users] Mopac7 / Gromacs 4.0.4 Issue

Gerrit, First, I realized that it didn't complete my thought about why the ./configure fails. ld is simply unable to find the -lmopac library. It seems that I have gotten around that by adding the mopac information into pkgconfig directory (by way of creating a .pc file and placing it into the /us

Re: [gmx-users] Membrane protein tutorial

Mark Abraham wrote: Justin A. Lemkul wrote: Pawan Kumar wrote: Hello Sir, The whole point in making an index file was to merge the sol and cl- ions. If i put popc also in the index file then it wont make any much useful group because lipids needs to be defined in a different group as I

Re: [gmx-users] Membrane protein tutorial

Justin A. Lemkul wrote: Pawan Kumar wrote: Hello Sir, The whole point in making an index file was to merge the sol and cl- ions. If i put popc also in the index file then it wont make any much useful group because lipids needs to be defined in a different group as I have read in various ar

Re: [gmx-users] Pressure Coupling Problem

On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> So I got my small water box (800 waters) to behave stably with pressure >> coupling after more minimization but I still can't get my large system to >> work with pressure coupling. I tried minimizing but I can never

Re: [gmx-users] Release of R.E.D. Server

What about use for commercial purposes? On Thu, Apr 9, 2009 at 1:31 AM, FyD wrote: > Dear All, > > I am pleased to announce the release of R.E.D. Server available @ > http://q4md-forcefieldtools.org/REDS/. > > R.E.D. Server provides the software and hardware (i. e. a cluster of > computers) requ

Re: [gmx-users] Pressure Coupling Problem

Joe Joe wrote: So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/wat

Re: [gmx-users] Pressure Coupling Problem

So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/water simulations of lar

Re: [gmx-users] Membrane protein tutorial

Respected Sir, Greetings from Pawan. It has worked now. I dint edit the index file before also. The problem was with the .mdp file. It was recognising lipids as POP and I gave as POPC in the .mdp file. Now there are no more errors. Thanks a lot. Thanking you, Pawan On Thu, Apr 9, 2009 at 3:35 PM

Re: [gmx-users] Re:pdb files and force field

Bhawana Gupta wrote: hello sir, Thankyou for the reply. The pdb file i had taken from the TINKER is the one where force field used is oplsaa. when i use this file in gromacs.it give error of atom type. It is always better to post the exact error message. What tool a

Re: [gmx-users] problem in increasing lipid bilayer size and to know about net charge on protein

nitu sharma wrote: Hi justin Thanks for tutorial of membrane protein simulation its very useful for us . But I want to ask two basic question - 1.The lipid bilayer I have downloded from teleman sir website is so small in comparision with my protein the suitable box vector

Re: [gmx-users] Membrane protein tutorial

Pawan Kumar wrote: Hello Sir, The whole point in making an index file was to merge the sol and cl- ions. If i put popc also in the index file then it wont make any much useful group because lipids needs to be defined in a different group as I have read in various archives. Please do correct

[gmx-users] Release of R.E.D. Server

Dear All, I am pleased to announce the release of R.E.D. Server available @ http://q4md-forcefieldtools.org/REDS/. R.E.D. Server provides the software and hardware (i. e. a cluster of computers) required for the derivation of highly effective and reproducible RESP and ESP atomic charge va

Re: [gmx-users] problem in increasing lipid bilayer size and to know about net charge on protein

Hi Nitu, 9 apr 2009 kl. 08.56 skrev gmx-users-requ...@gromacs.org: 2. I want to know the net charge present on my protein can u suggest me how can it become possible . Based on the protonation states and the termini you use in pdb2gmx the total charge is reported to stdout. Regards, Pär

[gmx-users] Re:pdb files and force field

hello sir, Thankyou for the reply. The pdb file i had taken from the TINKER is the one where force field used is oplsaa. when i use this file in gromacs.it give error of atom type. when i had gone in top folder which is in gromacs where all the force fields are defined. its written that you must