[gmx-users] two ligand itp file from ACPYPE

[Justin Lemkul]

On 2/19/14, 10:14 AM, ipek wrote:
> 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
> *********************************************

Your column alignment is wrong.  See http://manual.gromacs.org/online/gro.html.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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