Re: [gmx-users] Porting CHARMM topologies and parameters

Mark Abraham wrote: Jerome Henin wrote: Hi all, As quite a few people have done before, I am about to try and convert a CHARMM topology into a GROMACS one. To that effect, I will probably need one or several programs that will do part of the job. When these are done, I suppose they might be

Re: [gmx-users] Hi ..

Navratna Vajpai wrote: Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how

Re: [gmx-users] Porting CHARMM topologies and parameters

Jerome Henin wrote: Hi all, As quite a few people have done before, I am about to try and convert a CHARMM topology into a GROMACS one. To that effect, I will probably need one or several programs that will do part of the job. When these are done, I suppose they might be of interest to others

[gmx-users] incorporating fluorescent probes onto a protein

Hi friends!I have built a fluorescent probe using PRODRG and saved the coordinates without the hydrogens. 1. Must I save with hydrogens and charges?2. How to incorporate this onto cysteines. As the coordinates need to be adjusted to the location of Cys when put on the protein before I can perform a

[gmx-users] Porting CHARMM topologies and parameters

Hi all, As quite a few people have done before, I am about to try and convert a CHARMM topology into a GROMACS one. To that effect, I will probably need one or several programs that will do part of the job. When these are done, I suppose they might be of interest to others on this list. Since

Re: [gmx-users] Ligand binding energy using LIE with PME

Diane, Also, some of my inhibitors and complexes are charged. In my simulation of the complex, I have added a counterion (Na). Does this complicate matters worse ? For the inhibitors in water, I protonated the ligand, according to a procedure I saw in a paper. Ordinarily you want the system

[gmx-users] Re: steroid topology

Hi Diane Thanks for writing in. I guess I should have mentioned this earlier. To obtain partial charges for my substrate topology, I do an abinitio calculation (B-3LYP/6-31G*) and get the Chelpg and MKS charge distributions using Gaussian. Then I try and fit these charges to the steroid based on (

Re: [gmx-users] edit specbond.dat file

Hi Elias, Use a GROMOS96 force field (43a2, 45a3, or preferrably 53a5 or 53a6) or OPLS, or Amber... Let it depend on the question you want to answer. Do you want to compare with results previously obtained? Do you need all atoms, i.e. all hydrogens, or can you do with a united atom force field (a

[gmx-users] edit specbond.dat file

Message: 2Date: Tue, 15 Aug 2006 13:05:07 -0300From: "Elias santos" <[EMAIL PROTECTED] >Subject: [gmx-users] clusters [4Fe-4S]+2To: gmx-users@gromacs.orgMessage-ID:       < [EMAIL PROTECTED]>Content-Type: text/plain; charset="iso-8859-1"Hi !!I to construct to the block for residuo FS4 of the two cl

[gmx-users] conections Fe-S(Cys)

Hi  As I fill the fields of the archive specbond.dat for linkings between atoms of Fe of residue FS4 and SG of residuo of cystein Elias ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post

RE: [gmx-users] Ligand binding energy using LIE with PME

On the same subject, I have read in the list about long-range interactions (Coul-LR, LJ-LR) which are supposed to be included in the energy parameters calculated in g_energy, but I never see those. Do you have to write something specific in the .mdp files to get them ? Also, some of my inhibit

RE: [gmx-users] steroid topology

I am also working with steroids (but in my case, steroidal hybrid inhibitors) with the gmx force field. From my experience working with the PRODRG program, the topologies needed some modifications (for example the program assigns my phenol OH as a carbonyl and one aromatic bare carbon as a CH1)

[gmx-users] Energy Minimization nan && WARNING 1 [file "blah.itp", line 1020]: No default G96Angle types, using zeroes

dear gromacs users, i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme which is covalently bound to a piece of dna i.e. a tyrosine is connected to the dna backbone establishing a phosphodiester group. but each time i try to start the simulation using the G43a1 forcefield t

[gmx-users] Hi ..

Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how to get the HA (after or bef

Re: [gmx-users] problem with ambconv

Diane, I think we have used it with Amber 8 and Amber 9, probably also Amber 7, although in its current version it relies on being able to parse prmtop files, which means that it is dependent on the amber8/9 prmtop format. If this changed, it wouldn't work. I'll send it along in just a moment.

[gmx-users] Ligand binding energy using LIE with PME

Title: Ligand binding energy using LIE with PME Hi gmx-users I know that this has been discussed before from consultation of the mail archive, but there is still confusion : I want to obtain the ligand binding energy from my 1ns PME simulation of a ligand-protein complex. I have made, as di

Re: [gmx-users] trr and xtc specification

Martin Höfling wrote: Hello everybody, did I overlooked some piece of documentation in which these binary formats are described? Or do you have to read the gromacs sources to find information? Regards Martin There is some link on the website to the xtc format, but for details you ne

[gmx-users] trr and xtc specification

Hello everybody, did I overlooked some piece of documentation in which these binary formats are described? Or do you have to read the gromacs sources to find information? Regards Martin -- "Filme"? Ist das dieses neumodisches Zeugs, das wie Internet ohne klicken funktioniert? (Sven Tue

Re: [gmx-users] Hi..

Many thanks Eric, it worked. I didn't really had look into this.Best regardsNavOn Aug 16, 2006, at 11:34 AM, Erik Marklund wrote:On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote: Navratna Vajpai wrote: Hey Mark..I had attached the file along with the mail. I think you could not receive

Re: [gmx-users] Hi..

On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote: > Navratna Vajpai wrote: > > Hey Mark.. > > I had attached the file along with the mail. I think you could > > not receive it. let me paste the contents and explain it little more. > > I am trying to run the simulation in vacuum of a n

Re: [gmx-users] Hi..

Navratna Vajpai wrote: Hey Mark.. I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working

Re: [gmx-users] Hi..

Hey Mark..I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the

Re: [gmx-users] Hi..

Navratna Vajpai wrote: Dear All .. I have only recently started the GROMACS package. I want to run a MD simulation in vacuum for 5 ns say. I have tried to edit the demo file which comes with the GROMACS package. but Some how it give an error. Which I am still unable to solve. I am atttaching t

[gmx-users] Hi..

Dear All... I was trying to move further and finally managed to move forward. I am explaining the problem in little more detail. The problem arises when the grompp before the mdrun is executed. I don't know why but it ask for -n option for its execution. I tried that also but still the error stays.

[gmx-users] Hi..

Dear All .. I have only recently started the GROMACS package. I want to run a MD simulation in vacuum for 5 ns say. I have tried to edit the demo file which comes with the GROMACS package. but Some how it give an error. Which I am still unable to solve. I am atttaching the file under this. Could an

Re: Fwd: [gmx-users] Hen egg white lysozyme.

Viswanadham Sridhara wrote: Hello Dr.Spoel and others, There is one more problem with the simulation of hen egg white lysozyme simulation in water I am running. The timestep I could use is just 0.5 fs or 0.0005ps. Is there any way around to increase the timestep. This is how a part of my mdp f

Re: [gmx-users] water shell model

Luciano Costa wrote: Hi all and Spoel Based on mailing list answer at Mar 20th 2003, which discribed the entire topology file for water shell model, referencing on J. Phys. Chem B. 105 (2618) 2001, I have tryed to run water polarization MD with this file.itp. However, running grompp a message