Ligand minimization tool

I have minimized my protein using spdb viewer.But i am not able to minimize my ligand using same.pls suggest the tool or the way to minimize ligand using spdb viewer. or any tool or free software which minimizes using same forcefield used by spdbviewer

protein ligand minimization

• 2,934 views • link

written 9.9 years ago by ppnana •

See this post, it may help:

Ligand minimization Using prodrg

• 0 views • link

written 9.9 years ago by natasha.sernova

0 answers

No answers yet.

More posts like this

Magnesium ion in a post-docking adjustment
written 1.8 years ago by Rodolfo Adrián •

Hi, I was wondering if a post-docking adjustment of my Protein-Ligand (RNA) Model is validated: I performed a docking simulation with Autodock Vina v. 1.2.0, …
Forcefiled for methyl arsonous acid
written 3.3 years ago by Peerzada •

Hello all , I want to create the forcefield for methyl arsonous acid , as parameters for arsenic is not there in any of the …
Mauve Alignment Viewer
written 6.4 years ago by biohacker_tobe •

Hello community, I was able to conduct a multiple whole genome alignment of my strains with ProgressiveMauve, however I want to visualize my alignment possible …
vContact2 donwload and command line
written 6.5 years ago by vishalchanda364 •

Is there any way that I can download and use command line to run the vConTACT2 software for MCL-Clustering of protein homologies and putative viral …
protein modeling of metalloprotein
written 8.1 years ago by ppnana •

I am very much new to protein modeling and using a tool modeller and chimera.I have a model a protein for which the template has …
error 'LIG ' not found in residue topology database in gromacs how to solve
written 8.8 years ago by ppnana •

Hello All I am trying to minimize a ligand only without any protein which is cholesterol but it gives the following error FATAL ERROR Residue …
How can I align a generated ligand (from SMILES) to a ligand in a PDB?
written 9.3 years ago by brett.spurrier •

I have a ligand that exists in its own PDB (*reference PDB*). I have then generated another (structurally similar, but not exact) ligand from SMILES, …
Looking for a protein-rna docking tool
written 11.9 years ago by rohit.bioinfo.11 •

Dear all, I am going to dock my RNA as ligand with protein in auto dock.but a torsion problem show. My RNA shows 104 torsion …
Improved Metal Binding Upon Amino Acid Change
written 13.2 years ago by Alper Yilmaz

<p>Hi, I am trying to screen amino acid changes in a given protein and calculate if ligand binding has improved or not. I was searching …
Visualizing Genes On A Chromosome According To Their Position
written 13.9 years ago by Mandar •

<p>Hi all, i have 700 genes of drosophila and i want to show them all on the chromosome according to there position on linear scale. …