Questions tagged [molecular-dynamics]
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Sending chimera MD to remote computer
I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password)....
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Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
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Generating intercalation site in DNA for custom sequence
Thank you for your help.
Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
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Drug-DNA complex simulation using AMBER
I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...