[gmx-users] (no subject)

hello to all How can i perform PBSA in gromacs Thanks in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] (no subject)

Anyone if have idea, Kindly address On 28 Jun 2017 07:41, "Shivangi Agarwal" <shivangi.agarwal...@gmail.com> wrote: > Dear all gromacs users > > i have to define a new residue, i have added it in *residuetype.dat* file. > but still getting error: "residue

[gmx-users] (no subject)

I want to join gmx users so that i can ask and answer queries. please tell me how to join -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

[gmx-users] (no subject)

Hello I used the ATB server for generation of topology file following Gromacs Turorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

[gmx-users] (no subject)

Hello all How to handle HS14 generated by ATB server in topology file? Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] (no subject)

Hello to all gmx users I am performing protein ligand complex MD simulation but my protein structure has been broken during energy minimization process. What may be the suitable reason? How I can solve this? Your support is highly appreciated -- Gromacs Users mailing list * Please search the

Re: [gmx-users] (no subject)

> Hi, > > You don't need a file in the gro format. You need coordinates that match > the topology present in any supported file format, eg pdb or g96 etc. > > Mark > > On Tue, 20 Jun 2017 09:01 Shivangi Agarwal <shivangi.agarwal...@gmail.com> > wrote: > > > He

Re: [gmx-users] (no subject)

Hi But it is broken. .. strand with proline with three odr residues has been broken and visible... i have Checked in vmd and pymol On 21 Jun 2017 17:16, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: > Hi, > > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal < >

Re: [gmx-users] (no subject)

will be supplying parameters that belong > in the [atomtypes] directive, and their site needs to give you instructions > for how to get those recognized. Search their website and ask on their > support channel. > > Mark > > On Tue, Jun 20, 2017 at 3:21 PM Shivangi Agarwal < > shiv

[gmx-users] (no subject)

Hi all When i am generating a ligand topology using PRODRG, I am getting topology file with hydrogens deleted in it. Which another server can I use for ligand topology generation? Regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] (no subject)

Ya sir But for ATB, it is asking for total charge. How to calculate total charge? On 16 Jun 2017 18:59, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 6/16/17 8:03 AM, Shivangi Agarwal wrote: > >> Hi all >> >> When i am generating a ligand topolo

[gmx-users] (no subject)

shivangi.agarwal...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] (no subject)

Hello -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] (no subject)

of volume of protein hydration layer (Saumyak Mukherjee) 3. MD at different pH (Anu George) 4. Re: Using the md integrator for calculating free energy of solvation (Tasneem Kausar) 5. Re: MD at different pH (Nikhil Maroli) On Sun, Apr 30, 2017 at 12:50 AM, Shivangi Agarwal < shi

[gmx-users] (no subject)

Dear all gromacs users i have to define a new residue, i have added it in *residuetype.dat* file. but still getting error: "residue type not found". Kindly suggest -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Small ligand activators molecule

Hello everyone We want to design small molecule ligand activators for our protein of interest. What would be computational approach because we dont have any endogenous ligand available for that purpose. On structural basis how we would compare that particular ligand is going to act as an agonist