On Mon, May 18, 2020, sangita kachhap wrote:
>
>I am working on glycated oxy-hemoglobin.
>I have generated parameters for oxy-heme and N-terminal glycated-Valine.
>But when I am generating .prmtop and .inpcrd file, leap adding a "TER" card
>between N-terminal glycated-Valine (first residue) and Histidine (second
>residue).
>
>Since TER is adding within the chain, will it be problematic for further MD
>simulation?
You can use parmed to check if the bonding between the first and second
residue is correct.
Also, it's often safer to use ambpdb to create a pdb file from the
prmtop and inpcrd files, rather than using tleap's savePdb command. See
if that makes a difference for you.
....dac
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Received on Tue May 19 2020 - 05:00:03 PDT
