Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

Just in case. The order of atoms in your gro files should match the order in the top files.Like if we have 1 Protein and then 1 DMPC then again 1 PROTEIN and 1 DMPC, then top files should read as Protein 1 DMPC 1 Protein 1 DMPC 1 and so on... Hope this helps.

[gmx-users] RE: Re: Parameters for metals bonds inside proteins

Hi Diana Bredenberg and Nilsson Int journal of Quantum Chem 83, 230-244 2001 This paper describes modeling of Zinc Sulfhydryl bonds in Zinc fingers The zinc is tetrahedrally coordinated. Hope it helps. Alpay Date: Fri, 09 Jun 2006 15:51:03 +0200 From: David van der Spoel <[EMAIL PROTECTED]> S

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

> David, thanks for answering. > strange. i've installed one version of gromacs on the front end machinne > but > when it tries to run mprun_mpi it says that cannot find it (obvously > because > is searching on a node that is not the frontend machinne). > Where can i find a step by step example of

[gmx-users] Re: Verlet algorithm in GROMACS

Does GROMACS have velocity Verlet for an alternative? Jianwei I've got velocity verlet working on an older (3.1.4) version of GROMACS, and I've promised to eventually contribute it back to the main branch. All the developers agree that it will be good to eventually have velocity verlet as an

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

David, thanks for answering.strange. i've installed one version of gromacs on the front end machinne but when it tries to run mprun_mpi it says that cannot find it (obvously because is searching on a node that is not the frontend machinne). Where can i find a step by step example of working with gr

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

No ions, it's a neutral system. The order of DMPC and Water, in what sense? In the gro file, the proteins come first, then the DMPC residues, then the water. The order is similar in the [system] part of my top file. Are we allowed to send attachments on this user-list? If so, I'm more than

Re: [gmx-users] grompp warning: atom names don't match - with respect to solvent

Arneh Babakhani wrote: *Hello, I'm getting the following warning when running grompp:* processing coordinates... Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW) Warning: atom names in ../BuildInitialStructure/NoBa

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Francisco Tufró wrote: Hello list, My name is Francisco and I'm configuring a cluster to run gromacs using mpi. As far as i concern i have to install both gromacs and gromacs-mpi. The question is: do i have to install it on every cluster machinne? i have made some tests and it seems that the ans

[gmx-users] grompp warning: atom names don't match - with respect to solvent

Hello, I'm getting the following warning when running grompp: processing coordinates... Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW) Warning: atom names in ../BuildInitialStructure/NoBadWater.top and ../BuildI

Re: [gmx-users] Re: question about files

Have you followed the Drug-Enzime complex tutorial found at http://www2.umdnj.edu/~kerrigje/structbio_II.htm ? On Fri, 09 Jun 2006 20:40:28 +0200, David van der Spoel <[EMAIL PROTECTED]> wrote: > Robson Pacheco wrote: > > Dear Sirs > > > > I am new in molecular simulations, and I am experiencin

[gmx-users] Re: question about files

Robson Pacheco wrote: Dear Sirs I am new in molecular simulations, and I am experiencing many problems in generating topology files (GROMACS) for the systems I intend to study. I used The Dundee PRODRG Server in order to generate the files for a GROMACS run, however, the program pdb2gmx prompted

[gmx-users] Verlet algorithm in GROMACS

Hi, Seems GROMACS implements leap-frog version. What are the stored quantities, are they the current positions and velocities in the trajectory file? How do I restart a simulation at the exact point (position and velocity) of a previous simulaton. Does GROMACSD have velocity Verlet for an alterna

[gmx-users] Gromacs-mpi with Rocks v4.0

Hello list, My name is Francisco and I'm configuring a cluster to run gromacs using mpi. As far as i concern i have to install both gromacs and gromacs-mpi. The question is: do i have to install it on every cluster machinne? i have made some tests and it seems that the answer is yes, but i would l

Re: [gmx-users] L-J question

Anthony Cruz wrote: Hi users: I have a little question. I found some L-J parameters for heme iron for the GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5 and B (kJ nm^ -6 mol ^ -1) 8.886909e-

[gmx-users] Re: Parameters for metals bonds inside proteins

Diana Rodriguez Ortiz wrote: Hi, I thank you for your attention. I tried to use the mailing list but something has changed in that web page and I did not figure out how to enter my query. The metal is Zn and it is in a tetrahedral strucuture. It is not completely shielded from the enviro

[gmx-users] L-J question

Hi users: I have a little question. I found some L-J parameters for heme iron for the GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5 and B (kJ nm^ -6 mol ^ -1) 8.886909e-3. I need to make any

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Thanks again to your help. I will discuss these issues with my system administrator. I am really grateful for being a part of this excellent mailing list. Warm regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users"

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Alok wrote: Thanks a lot Dr. David Spoel :) I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It is running fine though with some warning. This time I specified the full path of mdrun_mpi binary. But now I am having one strange problem. Sometimes it runs smoothly and some

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Thanks a lot Dr. David Spoel :) I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It is running fine though with some warning. This time I specified the full path of mdrun_mpi binary. But now I am having one strange problem. Sometimes it runs smoothly and sometimes it does

[gmx-users] Re: Parameters for metals bonds inside proteins

Diana Rodriguez Ortiz wrote: Hi Mr. Spoel, I am working with a small protein (50 aminoacids) that has a metal atom near its center. Where can I find the parameters to be able to run a molecular dynamics of this protein? In this one, the metal is tied to 4 sulfurs I will run it with grom

Re: [gmx-users] compile GMX source code by VC 6.0

> > > Hi: > I tried to compile GMX source code by VC 6.0. > > I found the main function of MD simulation is in mdrun.c. And then i > compiled it as main file. > > But some varier type my compiler can not find . Such as : > LONG; > TCHAR; > BSTR; > BOOL; > DATE; Follow the instructions for con

Re: [gmx-users] Freezing part of the molecules!!!

Arneh Babakhani wrote: Can you use this freezegroups function during a minimizaiton? (say if you wanted to minimize solvent around your protein, while keeping the protein fixed?) please try before you buy, sorry before asking questions... this should work anyway. David van der Spoel wrote: