AMBER Archive (2009)

Subject: Re:Re: [AMBER] Error in minimal

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Tue Sep 15 2009 - 08:54:58 CDT


Dear case:
  I'm very appreciate for you to ansewer my question .I have checked that the inpcrd files which is exactly the one created at the same time as the prmtop file .I solvate my system as follows :
> solvateoct 1ooe TIP3PBOX 12
and the final line of the input coordinate file is :
  47.7317046 49.6938544 -7.5078304 48.5948508 49.3375349 -7.2974979
  47.1582457 49.3552439 -6.8202899
  96.6829838 96.6829838 96.6829838 109.4712190 109.4712190 109.4712190
I am very puzzled with this problem now,thank you very much !

2009-09-15case <case_at_biomaps.rutgers.edu> д
>On Tue, Sep 15, 2009, xuemeiwang1103 wrote:
>
>> ifbox=2 in prmtop but angles are not correct
>
>In brief: this indicates that the prmtop file was made with the solvateOct
>command (so you have a truncated octahedron), but that the coordinates do
>*not* seem to be for a truncated octahedron.
>
>We need information about what LEaP commands you used to solvate your system.
>This error probably has nothing to do with changes you made to the pdb file.
>
>A couple of quick points:
>
>1. double-check that the input coordinate file is exactly the one created at
>the same time as the prmtop file you are using.
>
>2. look at the final line of the input coordinate file, and let us know what
>is there.
>
>....dac
>
>
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