9 Questions 11 Answers 0 Followers
Questions related from Raghav Saxena
Dear all, I generated topology of a ligand (ATP) using Acpype which gave me the topology file topol.top and conf3_GMX.itp. I'm writing a report and confused as to what I should write in the...
04 April 2019 3,593 3 View
Dear all, Can we use the .itp file generated by Acpype with OPLS forcefield, is it compatible? I know Acpype uses antechamber which is based on GAFF but the question is whether the .itp file can...
02 February 2019 7,062 1 View
Dear all, I want to generate the topology for ATP(Mg2+) complex using OPLS-AA force field. For only ATP i used Acpype and it worked but when I used ATP(Mg2+) acpype is not working, that's...
01 January 2019 2,095 5 View
Dear all, I want to change only the color of an atom with index 10 in vmd and keeping rest of the atoms in default. Is there a way to do this in vmd? Thanks and Regards, Raghav
01 January 2019 3,310 2 View
Dear all, In VMD Dynamic Bond Representation the Bond Radius can't be set below 0.1. Is there a way to do it using TK console? I want to reduce the bond radius further to like...
01 January 2019 497 1 View
Dear all, Where can I get the structure of ATPMg+2 complex for my simulations? I need a starting structure for my MD simulations. Thanks and Regards, Raghav
01 January 2019 2,374 3 View
Dear all, In gromacs tutorial its written that pdb2gmx can be used for cofactors like NAD(H) and ATP, my question is how can i use it on my pdb file of ATP molecule. Do i need to change the...
01 January 2019 294 5 View
Dear all, I have this cp2k output file from a MD run MD-pos-1.xyz which has iteration number vs atomic coordinates information. I want to calculate charges for each atom for each...
11 November 2018 9,426 3 View
Dear all, I'm tying to solvate ATP molecule but I have failed In every attempt I made. I tried using amber and gromacs to solvate ATP but I get the error of unknown residue type...
11 November 2018 8,014 5 View
