[gmx-users] two ligand itp file from ACPYPE

[ipek]

Dear Justin;

Thank you for your comment. Here is a few lines from my conf.gro.

GROup of MAchos and Cynical Suckers
 5645
1p  C6N    1   0.044   0.083  -0.081
1p  H6N    2  -0.040   0.128  -0.027
1p  C5N    3   0.176   0.115  -0.046
1p  H5N    4   0.193   0.184   0.036
1p  C4N    5   0.283   0.061  -0.117
1p  H4N    6   0.384   0.090  -0.090
1p  C3N    7   0.259  -0.022  -0.229
1p  C7N    8   0.374  -0.067  -0.314
1p  O7N    9   0.487  -0.065  -0.263
1p  N7N   10   0.348  -0.104  -0.441
1p  H71   11   0.423  -0.134  -0.501
1p  H72   12   0.253  -0.099  -0.477
1p  C2N   13   0.129  -0.056  -0.260
1p  H2N   14   0.110  -0.120  -0.346
1p  N1N   15   0.023  -0.006  -0.185
1p C'N1   16  -0.114  -0.039  -0.234
1p H'N1   17  -0.112  -0.126  -0.300
1p C'N2   18  -0.219  -0.068  -0.130
1p H'N2   19  -0.220   0.004  -0.048
1p O'N2   20  -0.211  -0.203  -0.084
1p HON2   21  -0.261  -0.210  -0.002
1p C'N3   22  -0.344  -0.050  -0.215
1p H'N3   23  -0.436  -0.035  -0.158
*********************************************

And topology file start with;
; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"
; Include atomtypes
#include "atomtypes.itp"
; Include ligand1 topology file
#include "p.itp"
; Include ligand2 topology file
#include "FMT.itp"

**********************************

I have been looking for your fruitful suggestions.

Regards,

ipek

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