[AMBER] Helix Structures Lost during Heating and Equilibrium Steps

From: Bharat Manna <bharatmanna.gmail.com>
Date: Wed, 11 Sep 2019 16:13:38 +0530

Dear AMBER Users,

I was trying to simulate a small protein (~100 residues) containing 4
helices. During the heating (NVT) step (0K-300K), I found that two of the
helices lost the secondary structure and turned in to coils. At the time of
equilibrium (NPT) simulation, another one helix faced the same. I have
tried the standard ff14SB force field along with TIP3P/TIP4PEW water
models. In both cases, I found the same. Any suggestion, what might have
been gone wrong?

B Manna
PhD Scholar
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Received on Wed Sep 11 2019 - 04:00:01 PDT
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