[gmx-users] g_bond

[Dongsheng Zhang]

Dear David,

Thank you four reply. Since g_bond can read gro file as input. I amde
the following test. I made a short gro file test.gro as:

e100p64e100.pdb
  8
    1PEO     C1    1   4.069   2.093   1.068  0.1450  0.0605 -0.1344
    1PEO     C2    2   3.829   2.253   0.932 -0.0153 -0.1263  0.2339
    1PEO     C3    3   3.758   2.298   0.621  0.0345 -0.0676  0.0808
    1PEO     C4    4   3.597   2.147   0.396  0.3742  0.2042 -0.2398
    2PEO     C1    5   3.332   2.252   0.360 -0.1458 -0.0531 -0.3600
    2PEO     C2    6   3.243   2.412   0.104 -0.0849  0.1382  0.1444
    2PEO     C3    7   2.984   2.456  -0.060 -0.1546  0.3956 -0.0143
    2PEO     C4    8   3.080   2.278  -0.316  0.1942 -0.1982  0.3747
   5.64027   3.42476  11.12249

 My index file bond.ndx is :

[bond]
1	2
2	3
3	4

Then I tried to use:
g_bond -f test.gro -n bond.ndx

I got the error message:

Fatal error:
No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !


Could you please tell me where is the error? Thank you!


Dongsheng




On Wed, 2006-07-19 at 08:40 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Hello, GMX users,
> > 
> > When I tried to use g_bond -f *xtc -n *.ndx to get a bond length, I got
> > an error message as follows:
> > 
> > Fatal error:
> > No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
> 
> You probably have given the program an empty index file.
> All bonds have length 0 anyway.
> 
> > 
> > Could someone tell me what that means? Thank you in advance!
> > 
> > Dongsheng
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