[gmx-users] system contains proteins and DNAs with ffamber99

Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Gromacs add the hydrogen atoms of the water molecules? Additionly, when use Gromacs with the force field ffamber99, Can it add the hydrogen atoms of the DNA? Can I use the force field ffa

Re: [gmx-users] Seperation of specific trajectory from whole trajectory file.

minnale wrote: Hi all, I have run the protein simulation for 7ns with time interval 1ns each time, after that I catenated all the trj files by using trjcat command. Now I want to separate the 1ns .xtc from 7ns trajectory, is it possible to recover the 1ns trajectory file from entire

Re: [gmx-users] system contains proteins and DNAs with ffamber99

Dechang Li wrote: > Dear all, > > Sometimes,the PDB file contains water molecules which only have the > oxygen atom. Can > Gromacs add the hydrogen atoms of the water molecules? No - you'll be better off deleting them all, re-solvating using genbox and then doing a normal minimization & eq

Re: [gmx-users] system contains proteins and DNAs with ffamber99

hi, I think the answer to both of your questions is YES! Though, I have used ffamber03 for simulating protein+DNA. But I guess it shouldn't matter. Regards, Vignesh On Wed, Jun 11, 2008 at 3:50 PM, Dechang Li <[EMAIL PROTECTED]> wrote: > Dear all, > >Sometimes,the PDB file contains water mo

[gmx-users] system contains proteins and DNAs with ffamber99

If you have amber, you can make your topology in amber and convert them to gromacs with the script on this website: http://chemistry.csulb.edu/ffamber/tools.html kind regards, servaas Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Groma

[gmx-users] Re: still problems with dodecahedron box and editconf

Hi Jochen, > trjconv -ur compact worked out very well, thanks! Sebastian ___ 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! Pl

Re: [gmx-users] Simulating Protein+Dextran/PEG

Vigneshwar Ramakrishnan wrote: Dear All, I am a newbie to GROMACS and to MD simulations. I want to simulate and study protein in the presence of Dextran or PEG. 1. From literature and internet searches, I understand that PEG topology file can be generated using the PRODRG server and hence

Re: [gmx-users] system contains proteins and DNAs with ffamber99

Dear Dechang, in ff03 forcfield the nucleic acid parameters are the same as in the ff99. But ff99 forcefield for proteins is not the best choice due to it's 'helix friendly'nature. A better choice is to choose the ff03 forcfield for protein and dna, as well. hoe this helps. Balazs Mark Abraham írt

[gmx-users] Charmm_gromacs

Hi, I am trying to run gromacs using CHARMM force field. I downloaded "charmm_gromacs.tar.gz" file and I followed the instruction, that housed in "readme-charmmed-gromacs". I runned the command: pdb2gmx -ter -f -o -p , using as input file the *.gro file of the example, but the following error m

[gmx-users] pbc-replica exchange-trjconv

Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjconv -f fit.trr -o cluster.trr -n

Re: [gmx-users] pbc-replica exchange-trjconv

servaas michielssens wrote: Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjco

Re: [gmx-users] pbc-replica exchange-trjconv

Hi Servaas, > trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr I think there's quite a bit of reason to start calling you names here :) Assumedly, fit.trr means that it results from fitting the trajectory to a reference? So what does this do with your PBC? > I also tr

Re: [gmx-users] Charmm_gromacs

I think we have understood the problem...if it's not true I will write again... Thanks. Velia Minicozzi On Wed, June 11, 2008 12:12 pm, Velia Minicozzi said: > Hi, > I am trying to run gromacs using CHARMM force field. I downloaded > "charmm_gromacs.tar.gz" file and I followed the instruction, t

回复： Re: [gmx-users] 2D projection and corresponding conformation

Dear sir : I also know these,but can you give some detail procedure for obtaining the corresponding conformations? Thank you in advance! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear user: > We know that observing the sampled conformations in the subspace spanned > by the eigen

Re: 回复： Re: [gmx-users] 2D projection and corresponding conformation

xi zhao wrote: > Dear sir : > I also know these,but can you give some detail procedure for obtaining > the corresponding conformations? Thank you in advance! No, because you've told us no detail of your procedure to generate your eigensystem and to produce the (labeled) projected points. Once you

回复： Re: 回复： Re: [gmx-use rs] 2D projection and corresponding conformation

Dear sir: For example, I only simulated a protein, further, 1. using g_covar producing eigenvalue.xvg and eigenvec.trr for all Ca atoms 2 using g_anaeig producing 2d projection.xvg 3 how to obtain corresponding corformation in 2d projection using trjconv? these steps are normal, can

[gmx-users] how to simulate liquid-vapor interface of a solution at a low pressure

Hi all, I want to simulate the liquid-vapor interface of I lithium bromide solution at 303K and 0.008bar. First I put the solution to a cubic box and used NPT ensemble to simulate. Then, I enlarged the box to form two liquid-vapor interface,and used NVT ensemble, but the pressure is not