[gmx-users] Gromacs to AMBER

Hi all, Can any body know how to take Gromacs trajectories of protein ligand system to AMBER MM-PBSA and further calculate binding free energies using MM-PBSA.. Can any body suggest some tutorials..on this Cheers -- Sainitin D -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Gromacs to Amber trajectory

Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory

Re: [gmx-users] Gromacs to Amber trajectory

On 17/06/2011 2:57 AM, Raja Pandian wrote: Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl http://amb2gmx.pl script. I did simulation using Gromacs Package

Re: [gmx-users] Gromacs to Amber trajectory

Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory

Re: [gmx-users] GROMACS to AMBER

Hello, You can try VMD. I is able to write coordinates in a lot of format, including the dcd and crd ones. Both are readable by ptraj, I believe. Otherwise, you can have a look on OpenBabel. Be careful when you convert you trajectory into the Amber format. You probably have to include the box

[gmx-users] GROMACS to AMBER

Hello all. I would like to know if there is a way to convert .trr or .xtc files from GROMACS to .crd files (AMBER trajectory). Best regards, Edson. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] GROMACS to AMBER

Edson Fauth Vargas Filho wrote: Hello all. I would like to know if there is a way to convert .trr or .xtc files from GROMACS to .crd files (AMBER trajectory). I once wrote a script that does the opposite (mdcrd - xtc), so I imagine the opposite is possible, as well. You can assemble a

[gmx-users] gromacs versus amber boxsize

I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the

Re: [gmx-users] gromacs versus amber boxsize -correction-

Hi, On Tuesday, 29. January 2008 13:14, servaas michielssens wrote: I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 With -d and a triclinic box the size of the system in

Re: [gmx-users] gromacs versus amber boxsize

On Tue, 29 Jan 2008 12:57:13 +0100 servaas michielssens [EMAIL PROTECTED] wrote: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this,

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

Thank you for the good reference. ^^ On 8/14/07, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: JCTC December 2005, IIRC :-) YDRC...: JCC 26: 1701-1718 (December 2005) :p Tsjerk Mark ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

Hi Seungpyo Hong, Hi, gmx-users, Recently I have try to use AMBER 9 for the simulation of protein with about 300 residues. Surprisingly, I found that AMBER is far slower than GROMACS; GROMACS is about twice faster. I can not figure out the reason. Why is GROMACS faster than AMBER? Could

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

Tsjerk Wassenaar wrote: Hi Seungpyo Hong, Hi, gmx-users, Recently I have try to use AMBER 9 for the simulation of protein with about 300 residues. Surprisingly, I found that AMBER is far slower than GROMACS; GROMACS is about twice faster. I can not figure out the reason. Why is GROMACS faster

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

It is found on Gromacs' website http://www.gromacs.org/content/view/12/176/ Regards, Yang Ye - Original Message From: SeungPyo Hong [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Monday, August 13, 2007 9:12:47 PM Subject: [gmx-users] GROMACS vs. AMBER speed comparison? Hi, gmx

[gmx-users] Gromacs to amber atom type

In God We Trust Hello GMX users Does anyone know a way to convert atom type of G43a1 to atom type of Amber96(parm96) automatically. Thank you very much in advance Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran