[gmx-users] Simulating multiple fragments

Hi all I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box . I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully employ

[gmx-users] query about identifying representative snapshots from a 2D FEL

Dear Gromacs users I am interested in identifying the representative snapshots from a 2D Free energy landscape plot generated using g_sham using the reaction coordinates obtained from EV1 and EV2 projections. Can some suggest on how to back trace the coordinates from a 2D FEL and also the t

[gmx-users] constraints between protein ligand - metal chelation

Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and fi

Re: [gmx-users] constraints between protein ligand - metal chelation

materize the > complex as a single moleculetype and use distance restraints there, can't > you? > > > On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: > > Dear Gromacs users > > > > I was wondering if there exists any technique that sets > > distance rest

Re: [gmx-users] constraints between protein ligand - metal chelation

> > force strenght 1000J. >> > >> > Function 6 doesn't implie the generation of angles and dihedrals so it >> is >> > the right choice >> > to impose distance restraints >> > >> > >> > Francesco >> > 2012/5/20

[gmx-users] RIMSP calculation

Hi Gromacs users I am trying to measure the similarity of the subspace sampled by a mutant protein-Ligand complex versus a wild type complex based on the eigen vectors computed using PCA. I was wondering, does and handy scripts does exists to compute the root mean square inner product ( RMSIP)

Re: [gmx-users] RIMSP calculation

Hi Tsjerk Many thanks for your kind response. Got the script, will try to run it. Also thanks for clarifying RMSIP vs Cosine content values. Regards Vijayan.R On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar wrote: > Hi Vijayan, > > There must be a script somewhere in the archives > (http://w

Re: [gmx-users] Re: Attention:urgent

Plz be very specific about your problem. In fact iam not able to find out that problem is. what is the error msg what did you do do you need a sge script to submit job in a super computer or a cluster??? if so then what queing system all thes ethings are very imp On Thu, Jul 26, 2012 at 7:33 AM,

[gmx-users] SASA query

+ligand)** is this the right procedure. R.S.K.Vijayan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe req

[gmx-users] MM/PBSA Gromacs

Dear Gromacs users Is there any script that does a PB or GB calculation to perform a MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py script available in Amber. I find a similar question raised by a user a couple of years back. Any successful implementation Vijaya

[gmx-users] Cosine content

Dear Gromacs users I have a question regarding cosine content. I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. But when i perform a cosin

[gmx-users] Eigenvalue values from PCA (a general question)

Hi all I have a query about the eigenvalue values obtained from g_covar and g_anaeig I performed essential dynamics using PCA on my system (Protein-DNA complex) considering BB of the protein and the phosphate and sugar of the DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar wrote: > Hi Vijayan R., > > > What i infer from this is that the cumulative variance experienced by > the > > top 10 P

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Thanks Tsjerk On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar wrote: > Hi Vijayan.R, > > Not really. NMA also assumes linear relationships. > > Cheers, > > Tsjerk > > On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan > wrote: > > Hi Tsjerk > > >

Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

Thanks Micheal for pointing out the mistake On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel wrote: > >Date: Thu, 15 Dec 2011 15:11:12 -0500 > >From: "R.S.K.Vijayan" > >Subject: [gmx-users] Eigenvalue values from PCA (a general question) > >To: g

[gmx-users] discrepancy between ED motions and the MD motion

Hi all I carried out a distance analysis between two domains with respect to time based on the center of mass. Subsequently i also carried out a PCA based essential dynamics to identify the global/biologically relevant motions. The strange and inconsistent result i find here is when i calculate

Re: [gmx-users] discrepancy between ED motions and the MD motion

rse. > As a sidenote, do check whether it is a biologically relevant motion, or > merely relaxation. > > Cheers, > > Tsjerk > > On Dec 21, 2011 4:24 PM, "R.S.K.Vijayan" wrote: > > > Hi all > > I carried out a distance analysis between two domains wit

[gmx-users] mixing of PCs for generating reduced free energy profile using g_sham

Hi Gromacs user community a) I was wondering if it is possible to mix a common pair of PCs from two simulations (say, PC1 from a bound simulation vs PC1 from unbound simulation or for that matter wild vs mutant) as an reaction coordinates to generate a comparative reduced free energy profile u