16 Questions 21 Answers 0 Followers
Questions related from Bikash Ranjan Sahoo
Hi all, I am trying to coordinate zinc to the NMR structure PDB ID: 1sp1 (a C2H2 zinc-finger) using HADDOCK. To make it clear, the PDB structure is zinc coordinated, and I am using it as a system...
15 June 2023 3,707 1 View
Hi RG members, I found NTB buffer suitable to extract chromatin in buffer containing 1% SDS used for ChIP-seq experiments. I am wondering if anyone knows what is the composition of NTB buffer....
10 August 2021 2,869 1 View
Dear members, I am trying to express and purify a mouse-derived enzyme (rotamase A) having 7 X His-TEV cleavage site. The protein overexpression at 37C (0.8M IPTG induction for 3 hrs) shows a...
22 December 2016 6,072 3 View
I am working on T and B-lymphoma, and B16F1 melanoma cell lines. I would like to know if 2 uL is enough for 500 mL RPMI/DMEM +10% FCS+ 5.5mL antibiotic media culture system. Is it sufficient to...
26 April 2016 7,389 8 View
Dear all, I would like to count the number of cells from my OD600 values. The OD600 value for B. Substilis and S. epidermis are 0.5. Could somebody tell me how to convert these values to number...
11 February 2016 5,384 12 View
Dear all, I would like to cultivate Lactobacillus acidophilus from the L-dried sample. I do not have any experiences in culturing bacteria other than E. coli and my lab has no MRS media. Could...
15 January 2016 8,814 5 View
Dear All, I am trying to run US in gromacs for my protein-lipid system in version 5.0.2. I tried to simulate the same system using the attached pull.mdp file in Gromacs 4.6.x. It was running fine....
30 November 2015 3,945 4 View
Dear All,I have upgraded my Gromacs v4.5.5 to 5.0. I am unable to run parallel minimization and simulation in cluster. Previously (v4.5.5) I was simulating using the command “mdrun –v –s em.tpr...
05 December 2014 9,226 4 View
Dear RG members, Is it required to add counterions (Na+) to a MD system with negatively charged lipid molecules (POPG). Can I perform MD without adding counterions for my target...
10 October 2014 8,906 3 View
Dear RG members, I am trying to simulate the DOPC_128 (http://ambermd.org/tutorials/advanced/tutorial16/)following the steps described in Amber_16 tutorial. As I do not have access to Amber14, I...
22 September 2014 4,058 3 View
Dear RG-members, During MD simulation, after position restraint MD the covalent bond between the ligand and protein is missing. The ligand is covalently attached to the protein. But, in Gromacs...
20 August 2014 9,580 9 View
Kindly help me in interpreting the binding energy with its Ka, Kd and KD values. Using in silico methodology, I have computed the binding energy between the protein-ligand complex (-29.06 kJ/mol)....
10 April 2014 795 3 View
In some articles authors have carried out MD in Gromacs by slowly increasing the temperature. I wanted to perform such a technique for my work by increasing the temperature slowly from 300 to 310...
02 September 2013 2,304 18 View
I want to build the topology file of lipid and water. How to create the topology file of the attached dmpc.gro molecule by Gromacs? I don't want to download the dmpc_topol.top from Tieleman...
20 August 2013 2,740 3 View
do_dssp program is firing segmentation fault for the .trr file. Please help if you have sucessfully performed the SS analysis in Gromacs. Reading file md.tpr, VERSION 4.5.5 (single...
07 August 2013 9,495 4 View
Http://www.kazusa.or.jp/codon/
24 January 2013 6,066 3 View
