22 Questions 87 Answers 0 Followers
Questions related from Thirumal Kumar
I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?
08 August 2019 7,441 4 View
I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...
03 March 2019 6,377 4 View
I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...
03 March 2019 2,057 3 View
I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...
02 February 2019 3,204 5 View
We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...
04 April 2018 4,112 0 View
03 March 2018 7,206 1 View
Can someone suggest free online/offline tool to predict the drugliness of the multiple small compounds in sdf format? I tried DrugLito, but it is predicting incorrect values. So I am looking for...
06 June 2017 8,609 0 View
I have gone through the paper entitled "Quantifying the chemical beauty of drugs by Bickerton et al., 2012" but I am unable to understand the normal values for each parameter (MW, LogP, etc.)...
06 June 2017 7,857 0 View
When there is a set of parameters for drug-likeness such as MW, LogP, HBD, HBA, etc., why are some commercially available drugs which are known to best don't satisfy it?
06 June 2017 2,269 5 View
When I go with Gromacs protein simulations, should I consider about performing long run (at least 100ns) or multiple runs (at least 2 runs)? Which one of these could be more reliable and why?
04 April 2017 2,715 3 View
I usually add counter ions (Na or Cl) to neutralize system during dynamics but if a protein is already in neutral condition with a condition "No ions to add and no potential to calculate", what is...
03 March 2017 5,665 4 View
I used mindist of gromacs to find the distance between the proteins (native and mutants) and the metal (metalloprotein) over the simulation period. I have the output in form of graphs. Is there a...
03 March 2017 624 2 View
When there are two drugs of the same mechanism with different half-life, in this case, which drug should I choose and why?
12 December 2016 10,031 2 View
I have a native and mutant PDB files. How to find the percentage of alpha helix, beta sheet, turns etc., from the pdb file (not with the FASTA sequence)
11 November 2016 1,099 5 View
Is it possible to model a protein with deletion mutation? If YES, What could be the appropriate method? If No, what could be an alternative in silico approach?
10 October 2016 2,676 2 View
I have a compound synthesised. I need to find what all compunds could be its derivatives. So I need to know what all the possible changes that could happen to my compound...
09 September 2016 6,658 1 View
We have found few proteins in the cell (not human) and a drug to treat the cell. Is there an insilico way to find on which protein does my drug interacts (eg. Cytoscape)?
09 September 2016 3,500 15 View
I have contigs after sequencing. How to combine them as single and find the genes? Are there free tools for this analysis?
07 July 2016 305 4 View
I wish to study the pH determinant in molecular dynamics (Gromacs), So is there something got to do with pKa ? Can anyone please explain me, how pKa differs with SNP? (In general) Is there a...
07 July 2016 624 1 View
I wish to perform docking study with iron oxide (Fe2O3) nanoparticle. Is there a database or tool to obtain this?
06 June 2016 9,929 1 View
I am interested in knowing about the pH of system during simulation. Several forums have stated that .mdp has nothing to do with altering pH of the system and it got something to do with...
06 June 2016 5,144 6 View
I am studying a protein which has Cysteine in position 261 and there are reports on PTM at this position and converting to oxoalanine. There are other reports mention cys261arg mutation to be...
01 January 1970 4,831 3 View
