AMBER Archive (2005)

Subject: Re: Re: AMBER: bad atom type: H

From: alice (alicew616_at_citiz.net)
Date: Wed Jun 15 2005 - 20:35:00 CDT

Dear David A. Case,

        
        Thanks so much for your help.
        And about the problem I meet[bad atom type in md run(igb=2)], I finally get it through:

        Under the unfixed amber7(bugfix.7), I replaced "h, n, c" to "H,N,C"£¬¡¡and then it is run normally.

        I'still can't get it run under the fixed amber7(bugfix.7). No error find in the out file. I'm really puzzle about it.

===== 2005-06-15 08:09:00 =======

>On Wed, Jun 15, 2005, alice wrote:
>>
>> I use sander in amber7, and found the error "bad atom type: ca", I look up
>> the mailling list and fix the amber7 with bugfix.7.
>> and no "bad atom type: ca" error, but new error is "bad atom type: H".
>
>First, be sure that your system works when gbsa=0. That will help see if
>there are any other problems in the setup.
>
>According to the logic in mdread.f, the error above should not be able to
>occur: the program only prints "bad atom type" after it has checked to see
>if it is begins with "H". There may some memory overrun, but I would ask you
>to double check that you have reported the *exact* error message.
>
>....dac
>
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= = = = = = = = = = = = = = = = = = = =
                        

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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡alice
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡alicew616_at_citiz.net
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-06-16

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