32 Questions 46 Answers 0 Followers
Questions related from Bikash Ranjan Sahoo
Hi, I am wondering if synthetic human islet amyloid polypeptide (IAPP) can be prepared just like beta-amyloid using NH4OH instead of using HFIP. Concerns: 1- I am not allowed to use...
05 May 2018 3,889 1 View
Hi, I could see a peak around ~330 nm for the water sample (MilliQ). This looks strange and I am unable to find the problem. The excitation was 295 nm. We washed the cuvette throughly, but still...
09 September 2017 1,556 8 View
Dear RG members, I would like to study the interaction of polystyrene with a class of receptor proteins. I am intended to use coarse-grained MD simulation (Martini ff ) in Gromacs. I am struggling...
05 May 2017 2,052 4 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...
12 December 2016 6,724 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...
04 April 2016 4,457 9 View
Dear RG members, I have followed the miniPrep protocol for plasmid isolation for two E. coli strains of OD ~ 0.5 (BL21 and DH5a). The plasmid concentration measurement using NanoDrop showed a...
03 March 2016 3,572 8 View
Dear RG members, I am running MD simulation in GROMACS (GPU) in cluster using qsub. I would like to know when my program will finish which I can not monitor from the GUI. Could somebody help in...
03 March 2016 3,789 0 View
Dear RG users, I am writing for some assistance in generating a lipid bilayer membrane as per the user need. The present lipid databases contains generally 128/64 lipids or bigger. I would like to...
02 February 2016 7,369 5 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...
02 February 2016 2,687 11 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...
01 January 2016 534 5 View
Dear RG members, I would like to know how the body control the antimicrobial peptide (AMP) production during infection in a concentration dependent pathway. It is well known that, many of the AMPs...
12 December 2015 848 2 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....
11 November 2015 2,919 5 View
Dear all, Enclose here is the grapgh of PMF of a small drug molecule in two different lipid systems using Gromacs steered MD and Umbrella sampling methods. The PMF for both systems are showing a...
11 November 2015 942 0 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...
12 December 2014 5,216 5 View
Dear All, I have computed the rotation of a helix from its Ca-atoms using g_helixorient program. But, I am unable to interpret the results. There are 16 columns for all X Y Z rotations listed in...
11 November 2014 7,516 0 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 5,542 4 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...
09 September 2014 1,470 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...
08 August 2014 2,303 9 View
Dear RG members, I am trying to install AMBER in parallel in one cluster having ifort compiler. I am getting the error MPIF90 command not found. I read the configure2 file in AmberTools/src,...
07 July 2014 1,008 2 View
I am trying to run SANDER in parallel in cluster. In Gromacs, I used to run dplace -c 0-59 mdrun -v -s em.tpr -c em.pdb -nt 60 (here I was defining CPU numbers 0-60, and -nt was assigning the...
07 July 2014 8,161 3 View
I am trying to simulate my Protein-ligand complex using AMBER-FF. I tried all 94,96,99SB, GS etc in Gromacs. However, the ligand atoms like OM is not there. So I have added the required atoms in...
04 April 2014 7,805 8 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)....
04 April 2014 8,864 3 View
I have calculated the BE of a small ligand (mol wt ~320 g/mol) with its receptor. The BE I have obtained was ~670 kJ/mol (~160 kcal/mol). I am little afraid of such a high value for the BE. Is...
01 January 2014 3,403 4 View
Dynamite: a simple way to gain insight into protein motion.(http://journals.iucr.org/d/issues/2004/12/01/ba5065/ba5065bdy.html) I wanted to perform some MD analysis using Dynamite program....
10 October 2013 9,860 0 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...
09 September 2013 6,199 19 View
How to run APBS in cluster (>50 CPU)? I want to perform apbs calculations (both polar and non polar) in cluster.
09 September 2013 10,051 0 View
I want a big DMPC lipid system (>256 DMPC) for my protein to do MD using Gromacs 4.5.5. However I am not able to combine two DMPC molecules along with water as presented in Tieleman sites. Pleas...
08 August 2013 1,027 8 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...
08 August 2013 9,884 4 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...
08 August 2013 9,211 4 View
NMR versus X-ray crystallography
05 May 2013 2,787 8 View
Http://www.kazusa.or.jp/codon/
01 January 2013 3,530 4 View
Dear all, I am wondering if my purified chaperone protein (Hsp104) is stable in -80 C. I tried to store it in for few days right after the AKTA-FPLC. I dry-freeze the AKTA products containing the...
01 January 1970 6,468 3 View
