Re: [AMBER] parameter for modified residue

From: David A Case <>
Date: Tue, 19 May 2020 07:43:40 -0400

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
>Since TER is adding within the chain, will it be problematic for further MD

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.


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Received on Tue May 19 2020 - 05:00:03 PDT
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