[AMBER] Problem with CPPTRAJ (RMSD)

From: Rui Chen <rchen6.ualberta.ca>
Date: Mon, 2 Sep 2019 23:21:47 -0600

Hello,

I have a problem to use CPPTRAJ to calculate the RMSD using the first frame
as the reference frame.
Basically, there are two problems:
1.
[image: Screen Shot 2019-09-02 at 11.10.28 PM.png]
I prepared the protein (generate parmtop and inpcrd files) using AMBER
force filed, run MD simulation using NAMD with AMBER inputs. So, after
production, the coordinate file I generated was in CHARMM format, dcd file.
I have 1000 frames in the dcd file, maybe because it's not AMBER format,
CPPTRAJ only read 123 frames. What should I do? Maybe I need to convert dcd
into AMBER format? How to do that?

2.
[image: Screen Shot 2019-09-02 at 11.11.11 PM.png]
Is the second warning about unit cell a big deal? How can I correct it?

Looking forward to hearing from you.

Best regards,
Rui





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Screen_Shot_2019-09-02_at_11.10.28_PM.png
(image/png attachment: Screen_Shot_2019-09-02_at_11.10.28_PM.png)

Screen_Shot_2019-09-02_at_11.11.11_PM.png
(image/png attachment: Screen_Shot_2019-09-02_at_11.11.11_PM.png)

Received on Mon Sep 02 2019 - 22:30:01 PDT
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