[gmx-users] CTP .gro and .itp file

[Mohsen Ramezanpour]

Dear All,

I am interested in doing MD simulation on protein and CTP molecule,
preferably in amber99sb-ildn ff in Gromacs. Well, I think we can also use
GAFF for CTP in combination with amber99-sb-ildn for protein. Please
correct me if I am wrong.

There are parameter files for ATP and GTP in .prep and .frcmod formats in
http://www.pharmacy.manchester.ac.uk/bryce/amber.
I have also .prep and .frcmod files for CTP from a published work.

I found relevant useful discussions in mailing list, for ATP though:
adding ATP parms to AMBER99
<http://news.gmane.org/find-root.php?message_id=ACC2149A%2d84F7%2d4E02%2d9E9E%2d0D4D2548F0FC%40berkeley.edu>
by
Stephen(2014-04-11),
acetonitrile from amber to gromacs
<http://news.gmane.org/find-root.php?message_id=4BF40EA1.7020008%40zib.de> by
Vedat (2010-05-19),
ATP for
<http://news.gmane.org/find-root.php?message_id=4e22679c1002042237v1bd8797bhc0dc6ddb03736569%40mail.gmail.com>
by
Chandan ( 2010-02-05).

However, before going through all file transform process between amber and
Gromacs, I was wondering if there is any parameter file (.gro and .itp)
available for CTP around or if there is any database I can find there.

Thanks in advance for your comments
Cheers
Mohsen




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