AMBER Archive (2006)

Subject: AMBER: How did the coordinates change in xleap?

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Tue Oct 17 2006 - 10:03:47 CDT

Dear All,

        When I compared the coordinates in inpcrd file with the corresponding ones in original pdb file, I found that they are very different, moreover, the coordinates in diffirent inpcrd file resulted from diffirent solvation condition (such as diffirent buffer value, add counter ions or not) are also diffirent, it looks like that original coordinates were transformed in xleap. Here I want to know that:

In which step did the transformation of coordinates take place? loadpdb, solvate or saveamberparm ? and how did the transformation go on?

    Any advice will be greatly appreciated! Thanks in advance & Best regards!

    yours sincerely, Zhihong Yu

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