Re: [gmx-users] Issue with RMSD for protein drug complex

2013-07-04 Thread Sainitin Donakonda
Hi Justin, Thank your very much for reply i have done both ways i also have backbone RMSD data so i will consider only this in my analysis. Cheers, Sainitin On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul wrote: > > > On 7/4/13 5:17 AM, Sainitin Donakonda wrote: > >> Hi all, >> >> I ran 20ns si

Re: [gmx-users] Issue with RMSD for protein drug complex

2013-07-04 Thread Justin Lemkul
On 7/4/13 5:17 AM, Sainitin Donakonda wrote: Hi all, I ran 20ns simulation on protein drug complex..now i want to check overall stability of this complex to acheive this i did following i supplied index file and choose Protein_Lig option for both least square fit and RMSD calculation..i used f

[gmx-users] Issue with RMSD for protein drug complex

2013-07-04 Thread Sainitin Donakonda
Hi all, I ran 20ns simulation on protein drug complex..now i want to check overall stability of this complex to acheive this i did following i supplied index file and choose Protein_Lig option for both least square fit and RMSD calculation..i used following command g_rms -f em.tpr (intital struct