Aashish Bhatt

7 Questions 13 Answers 0 Followers

Questions related from Aashish Bhatt

How to read gaussian fchk file?

I have run the required calculation for the force constant value in Gaussian successfully and have converted the file.chk file into fchk via formchk. So is there any software which can give...

04 April 2018 844 0 View

How can calculate resp charge?

I want to know how calculate the resp charge. I have followed the tutorial for understanding of resp charges in amber 16. For calculating the charge i have used only "linker part"...

11 November 2017 4,234 1 View

During simulation of glucose O5 atom and anomeric OH group are getting attached together.what could be possible reason?how important is charge?

I am facing a problem in (0GA+ROH) GLYCAM carbohydrate parameter while doing force field preparation for glucose molecule in AMBER. I have used Gaussian optimized structure and calculated the MK...

11 November 2017 3,132 0 View

How can i plot graph in xmgrace?

I have two different set of graph one set is starting from 0-200 and one set is 0-200 on x-axis. how can i merge both sets in xmgrace so that the total graph should be 0-400. means the x axis has...

11 November 2017 1,831 1 View

Why serine amino acid is behaving like a positive entity in protein electropotential surface?

I have serine aa in the core of protein behaving as a positive entity which i inferred from electropotential surface. as it contain OH negative its should behave as negative entity. I am not able...

10 October 2017 8,455 1 View

What is the meaning of EPW in water box ?

When I solvate the protein in AMBER16. EPW H2O shown in (AMBER output file) solvated PDB file.I don't understand what is the meaning of EPW. I have attached screenshot. kindly let me know.

01 January 2017 5,615 0 View

How can set a parameter for Ag+ ions in AMBER16?

I have try to simulate a protein with Ag+ ion with ff14SB at AMBER16. When I type in tleap script they showing message vdw parameter is not find. how can I set a parameter for Ag+ ions. please...

01 January 2017 7,721 4 View