[gmx-users] ADP topology parameter

[Zhiguo Liu]

Dear gmx-users ，

    

>Hi,
>I used PRODRG for GTP/GDP topology and it was right!
>Check your starting PDB coordinates both for PRODRG and further energy 
>minimization.
>Anyway, I think there should be a topology for ADP in GROMOS96...
>Hope this help,
>Ruben
Could you be so kind to send me a few sample topol and gro files of your GDP? 
Appreciate a lot!
And to my knowledge, seemingly there is only topologies for ATP and NADP in Gromos96, but no for ADP...




>
>Daan van Aalten wrote:
>
>>Hi Zhiguo
>>
>>You don't say what you use for input - remember the server cannot correct
>>for mistakes in either PDB file or 2D structure input. I.e. it works with
>>the GIGO principle (Garbage-In-Garbage-Out). In my experience, 9 out of 10
>>times when things go wrong it is because of inconsistencies in the user
>>input....
>>
>>Daan

This is my input for dundee server, is there any mistake in it?

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HETATM    1  PB  ADP  2001     -10.922  23.177  81.000  1.00 32.94           P  
HETATM    2  O1B ADP  2001     -11.708  22.755  79.793  1.00 30.32           O  
HETATM    3  O2B ADP  2001     -10.446  22.008  81.842  1.00 35.66           O  
HETATM    4  O3B ADP  2001     -11.704  24.214  81.811  1.00 30.64           O  
HETATM    5  PA  ADP  2001      -9.492  25.355  79.860  1.00 31.65           P  
HETATM    6  O1A ADP  2001      -9.338  25.363  78.374  1.00 30.48           O  
HETATM    7  O2A ADP  2001     -10.643  26.217  80.297  1.00 29.26           O  
HETATM    8  O3A ADP  2001      -9.568  23.870  80.508  1.00 32.35           O  
HETATM    9  O5* ADP  2001      -8.152  25.875  80.518  1.00 31.77           O  
HETATM   10  C5* ADP  2001      -7.997  25.879  81.925  1.00 32.00           C  
HETATM   11  C4* ADP  2001      -7.210  27.120  82.337  1.00 31.28           C  
HETATM   12  O4* ADP  2001      -5.956  27.180  81.667  1.00 29.26           O  
HETATM   13  C3* ADP  2001      -7.926  28.411  81.989  1.00 32.01           C  
HETATM   14  O3* ADP  2001      -8.955  28.733  82.907  1.00 33.25           O  
HETATM   15  C2* ADP  2001      -6.772  29.374  81.920  1.00 30.14           C  
HETATM   16  O2* ADP  2001      -6.406  29.720  83.239  1.00 34.66           O  
HETATM   17  C1* ADP  2001      -5.671  28.537  81.320  1.00 30.76           C  
HETATM   18  N9  ADP  2001      -5.607  28.641  79.863  1.00 30.69           N  
HETATM   19  C8  ADP  2001      -6.342  27.878  78.987  1.00 31.98           C  
HETATM   20  N7  ADP  2001      -6.041  28.235  77.706  1.00 30.56           N  
HETATM   21  C5  ADP  2001      -5.126  29.207  77.787  1.00 28.06           C  
HETATM   22  C6  ADP  2001      -4.499  29.902  76.794  1.00 30.48           C  
HETATM   23  N6  ADP  2001      -4.700  29.586  75.497  1.00 27.18           N  
HETATM   24  N1  ADP  2001      -3.609  30.863  77.166  1.00 30.36           N  
HETATM   25  C2  ADP  2001      -3.341  31.141  78.492  1.00 32.40           C  
HETATM   26  N3  ADP  2001      -3.970  30.432  79.483  1.00 31.40           N  
HETATM   27  C4  ADP  2001      -4.835  29.467  79.126  1.00 29.64           C  

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