Re: [AMBER] how to convert (psf) to (prmtop) and (incprd)

From: David A Case <>
Date: Sat, 12 Dec 2020 21:59:32 -0500

On Sat, Dec 12, 2020, Pinky Mazumder wrote:
>Do you have any idea how I could fix this issue?

Use the check command in cpptraj to find out which bonds have bad
initial bond lengths. Look at some of those visually before and after
the minimization. It's possible that things are OK after minimization
(the bond energy is much lower), but, as Carlos noted, bad things can
happen with poor starting structures, so you should try to figure out
what is going on: why does your initial structure have such bad bond


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Received on Sat Dec 12 2020 - 19:00:04 PST
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