[gmx-users] help

[Justin A. Lemkul]

qwang at mail.uh.edu wrote:
> Hi,
> I am trying to simulate a protein with a DPC micelle. Part of pdb files is:
> 
> CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
> ATOM      1  N   DPC M   1     -16.481  21.283  -0.739  1.00  0.00      MICE
> ATOM      2  C14 DPC M   1     -15.620  20.082  -1.136  1.00  0.00      MICE
> ATOM      3  C15 DPC M   1     -17.727  20.772  -0.234  1.00  0.00      MICE
> ATOM      4  C16 DPC M   1     -15.792  22.061   0.317  1.00  0.00      MICE
> ATOM      5  C17 DPC M   1     -16.780  22.230  -1.919  1.00  0.00      MICE
> ATOM      6 H141 DPC M   1     -14.613  20.409  -1.348  1.00  0.00      MICE
> ATOM      7 H142 DPC M   1     -16.000  19.717  -2.079  1.00  0.00      MICE
> ATOM      8 H151 DPC M   1     -18.375  21.592   0.038  1.00  0.00      MICE
> ATOM      9 H152 DPC M   1     -17.513  20.198   0.656  1.00  0.00      MICE
> 
> But when I use the command pdb2gmx, it is said "Residue 'DPC' not found 
> in residue topology database". How can I deal with it? Thank you.

This is probably the most common question asked on this list.  As such, when 
encountering problems, please do the following:

1. Search the list archive (www.gromacs.org, click "Search")
2. Search the wiki site (wiki.gromacs.org)

If you cannot resolve your problem with the above, at least give your email an 
appropriate subject line so it does not get shifted to the trash folder of an 
otherwise helpful individual who is not alerted to the question.  Usually 
subjects like "help," "error," of "I don't know what to do" get ignored because 
the answer can be solved by doing #1 or #2 above.

That said, I'll give you a hint: search the wiki, the answer is there.

-Justin

> 
> sincerely yours,
> Wang Qian
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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