[EMAIL PROTECTED] 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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