Re: [gmx-users] gromacs demo

> On 1/3/13 6:06 AM, amna khan wrote: > >> hi all. >> >> i am a beginer user of ubuntu and gromacs >> i installed gormacs on ubuntu 12.10 and now want to run demo , i dont know >> how to run this correctly >> >> i do by typing cd /usr/share/gr

Re: [gmx-users] dna-drug simulations

iled are same * how to reomve this error for groamcs 43a1 or amber or chrm forcefield On Sat, Jan 26, 2013 at 6:13 PM, Justin Lemkul wrote: > > > On 1/26/13 4:18 AM, amna khan wrote: > >> hi, all , >> >> i want to simulate dna with ligand/drug >> >> i a

Re: [gmx-users] bad box error

so, i could i correct this ? On Wed, Jan 30, 2013 at 12:52 AM, Justin Lemkul wrote: > > > On 1/29/13 2:43 PM, az kalsom wrote: > >> hi , >> >> when i use "editconf" to generate a dodecahedron box with the command >> >> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 >> >> the output

Re: [gmx-users] bad box error

1/29/13 3:07 PM, amna khan wrote: > >> so, i could i correct this ? >> >> > Probably, but we need a lot more information if you want help: > > 1. Describe what your system is and how you constructed conf.gro > 2. Post the first 3 and last 3 lines of conf.gro > 3.

Re: [gmx-users] bad box error

yes i have following this tutorial , the only difference i made is that i didn't change the charges for ligand file. it seems it is necessary to do this ? am i rite ? On Wed, Jan 30, 2013 at 1:51 AM, Justin Lemkul wrote: > > > On 1/29/13 3:46 PM, amna khan wrote: > >&

Re: [gmx-users] rtp topology file for ligand

ue, Feb 19, 2013 at 5:58 PM, Justin Lemkul wrote: > > > On 2/19/13 4:23 AM, amna khan wrote: > >> hi all, >> >> i generated the .itp file for my ligand using ATB, >> and i have generated the protein topology file by using the forcefield 13 >> >> m

Re: [gmx-users] rtp topology file for ligand

are 0_NFPHO 36 -0.376 -0.128 0.141 0_NFP C26 37 -0.328 0.137 -0.081 0_NFP C27 38 -0.293 0.373 -0.168 9.21266 2.62220 3.05500 what is woring with ligand to gro converion ? why this bad box error arose ? regards amna khan * On Tue, Feb 19, 2013

Re: [gmx-users] about simulation runs

2230 atoms and same as tutorial On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul wrote: > > > On 3/4/13 11:20 AM, amna khan wrote: > >> hi, >> i want to ask i have i3 laptop >> i want to run the 1ns simulations >> how much time it will take ? >> >&g

Re: [gmx-users] about simulation runs

and what about gromacs webserver ? can i submit all my prepared files there ? On Mon, Mar 4, 2013 at 10:27 PM, amna khan wrote: > 2230 atoms and same as tutorial > > > > > On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul wrote: > >> >> >> On 3/4/13 11:2

[gmx-users] dna-simualtions with gromacs

Complex_b4em.pdb –nname Na –nn 8 –g trp_ion.log rest step can i continue from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html please help me i am stuck at this step regards amna khan -- gmx-users mailing listgmx-users@gromacs.org http