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Questions related from Raghav Saxena
Dear experts, I am a newbie to NEB calculation and VASP. I am trying to study decomposition of HNNOH molecule to nitrogen (N2) and water (H2O). Although my images look correct with no overlapping...
28 May 2022 7,866 4 View
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 5,130 3 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...
29 January 2019 3,205 4 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
18 January 2019 4,326 2 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...
08 January 2019 636 5 View
