Re: [AMBER] Fw: covalent molecule and modified residue parameters

From: David A Case <>
Date: Mon, 7 Sep 2020 11:57:45 -0400

On Mon, Sep 07, 2020, Sarah Jane wrote:

>> HAR = sequence {ACE HAR NME}

Again, don't reuse the idenifier "HAR". Just type something like:

    x = sequence {ACE HAR NME}

Now the simplest thing to do is to use the bond command to add any
missing bonds. If you are going to be using the HAR residue a lot, you
could use tleap to set the connect0 and connect1 atoms to the N and C
atoms of the HAR residue (then use saveOff to save this as an off file
for use later.) But try the simpler thing first.

After you create a prmtop file, use parmed to ensure that you have the
bonds you want.


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Received on Mon Sep 07 2020 - 09:00:05 PDT
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