Re: [gmx-users] inquiring for solving trjconv problems

2013-01-20 Thread Mehdi Bagherpour
I am so grateful for your help sincerely On Mon, Jan 21, 2013 at 5:24 AM, Justin Lemkul wrote: > > > On 1/20/13 8:34 PM, Mehdi Bagherpour wrote: > >> excuse me Dear Justin >> >> I could not understand exactly what to do? >> My simulation system is DNA in water. >> >> > The -center option is con

Re: [gmx-users] inquiring for solving trjconv problems

2013-01-20 Thread Justin Lemkul
On 1/20/13 8:34 PM, Mehdi Bagherpour wrote: excuse me Dear Justin I could not understand exactly what to do? My simulation system is DNA in water. The -center option is convenient when you have to center a single molecule within a unit cell. If you have two molecules or more that you wish

Re: [gmx-users] inquiring for solving trjconv problems

2013-01-20 Thread Mehdi Bagherpour
excuse me Dear Justin I could not understand exactly what to do? My simulation system is DNA in water. when I use from bellow command I choose DNA group. In 25000 snapshot approximately in 1000 of this structures two strands of DNA are separated. * trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol

Re: [gmx-users] help with building DNA in gromacs

2013-01-20 Thread Justin Lemkul
On 1/20/13 3:57 PM, Tom wrote: Dear Gromacs User I built DNA with the pdb file and *mol2 But when I used pdb2gmx to obtain *top file, pdb2gmx give error report when I chose charmm27: --- Program pdb2gmx, VERSION 4.5.5 Source code file: resall.c, line: 581 Fatal error: R

[gmx-users] Simulation of the Rhodopsin-retinal complex

2013-01-20 Thread James Starlight
Dear Gromacs Users! I want to simulate sensory rhodopsin which in the ground-state contains cys-retinal covalently bonded to the polypeptide mainchain of photoreceptor via Shiff base. Now I'm looking for reasonable parameters of that retinal cofactor group for charmm ( 27 or 36 force field) I'll

Re: [gmx-users] inquiring for solving trjconv problems

2013-01-20 Thread Justin Lemkul
On 1/20/13 7:34 AM, Mehdi Bagherpour wrote: I use bellow commands but still in some of snapshot trajectories, two strand of DNA separated from each other in VMD. trjconv -s md.tpr -f md.xtc -o md.pdb -center trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact trjconv -s md.tpr -f md

Re: [gmx-users] inquiring for solving trjconv problems

2013-01-20 Thread Mehdi Bagherpour
I use bellow commands but still in some of snapshot trajectories, two strand of DNA separated from each other in VMD. trjconv -s md.tpr -f md.xtc -o md.pdb -center trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center -ur compact trj