Re: [gmx-users] LIGAND TOPOLOGY

2013-08-27 Thread Justin Lemkul
On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote: Dear users, I have been trying to build la ligand topology of my ligand through the PRODRG web server. I have the following queries; According to Justin's important tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl

[gmx-users] LIGAND TOPOLOGY

2013-08-27 Thread MUSYOKA THOMMAS
Dear users, I have been trying to build la ligand topology of my ligand through the PRODRG web server. I have the following queries; According to Justin's important tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html i am lost on how to allocat

Re: [gmx-users] ligand topology error

2013-02-01 Thread Justin Lemkul
On 2/1/13 9:37 AM, az kalsom wrote: hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation

[gmx-users] ligand topology error

2013-02-01 Thread az kalsom
hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that e

Re: [gmx-users] ligand topology

2013-01-31 Thread Justin Lemkul
On 1/31/13 9:51 AM, az kalsom wrote: hi i have docked the compund with protein and selected the best protein-ligand conformation for simulations, but when i generate the topolgy for ligand by Automated Topology Builder (ATB) and Repository , job is killed every tym. error message is 1) geomet

Re: [gmx-users] Ligand topology in topol.top

2011-11-01 Thread Steven Neumann
On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Guys, >> I am using Charmm27 ff for my protein and ligand system.

Re: [gmx-users] Ligand topology in topol.top

2011-11-01 Thread Justin A. Lemkul
Steven Neumann wrote: On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I include

Re: [gmx-users] Ligand topology in topol.top

2011-11-01 Thread Steven Neumann
On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Guys, >> I am using Charmm27 ff for my protein and ligand system. I used >> SwissParam to generate the topology for my ligand. I included the obtained >> topology of my ligand as in Justin tutorial: >> >>

Re: [gmx-users] Ligand topology in topol.top

2011-11-01 Thread Justin A. Lemkul
Steven Neumann wrote: Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include "posre.itp"

[gmx-users] Ligand topology in topol.top

2011-11-01 Thread Steven Neumann
Hi Guys, I am using Charmm27 ff for my protein and ligand system. I used SwissParam to generate the topology for my ligand. I included the obtained topology of my ligand as in Justin tutorial: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand topolo

Re: [gmx-users] ligand topology

2007-08-28 Thread Diego Enry
On 8/28/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote: > > > hello all, > > How to get the topology for a ligand, for which there is no information > available with the gromacs default libraries!! Please search the archive at http://www.gromacs.org/search before posting. A good start would b

Re: [gmx-users] ligand topology

2007-08-28 Thread Justin A. Lemkul
Quoting Blaise Mathias-Costa <[EMAIL PROTECTED]>: > hello all,How to get the topology for a ligand, for which there is no > information available with the gromacs default libraries!! Thanks in > advanceBlaise Try PRODRG: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ -Justin ==

[gmx-users] ligand topology

2007-08-28 Thread Blaise Mathias-Costa
hello all,How to get the topology for a ligand, for which there is no information available with the gromacs default libraries!! Thanks in advanceBlaise___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users P