Re: [gmx-users] Adding hydrogen

2013-09-29 Thread Justin Lemkul
On 9/28/13 9:41 PM, Abu Naser wrote: Hi all users, Is it possible to add hydrogens to some of the selected atoms in the system using pdb2gmx? pdb2gmx is a rather complex way to do it. g_protonate is the tool for adding hydrogens to a configuration, but note it can only handle PDB files at

[gmx-users] Adding hydrogen

2013-09-28 Thread Abu Naser
Hi all users, Is it possible to add hydrogens to some of the selected atoms in the system using pdb2gmx? With best regards, Naser -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please sear

Re: [gmx-users] adding hydrogen

2012-01-25 Thread Krzysztof Kuczera
I recommend the CHARMM-GUI website from Wonpil Im's group http://www.charmm-gui.org/ - use the 'PBD reader' tool Krzysztof On 1/25/12 4:29 AM, lina wrote: Hi, are there some tips of quick adding missing atoms ( namely hydrogens, non-titrable ones, or some ligands ones) ? Thanks, -- Krz

[gmx-users] adding hydrogen

2012-01-25 Thread lina
Hi, are there some tips of quick adding missing atoms ( namely hydrogens, non-titrable ones, or some ligands ones) ? Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Adding hydrogen

2006-06-12 Thread David van der Spoel
Sheng Yong yang wrote: Hi, Dear Gromacs Users, Seems pdb2gmx just can add hydrogen to the main chain, not side chain (one can check the tutor demo file). I wonder whether it is not necessary to add hydrogen on the side chain in Gromacs or one has to add the side chain hydrogen by other software.

[gmx-users] Adding hydrogen

2006-06-11 Thread Sheng Yong yang
Hi, Dear Gromacs Users, Seems pdb2gmx just can add hydrogen to the main chain, not side chain (one can check the tutor demo file). I wonder whether it is not necessary to add hydrogen on the side chain in Gromacs or one has to add the side chain hydrogen by other software. I appreciate very much if