hydroxyls in phosphate group collapsing

From: Yvonne.Westermaier_at_unige.ch
Date: Mon Jul 27 2009 - 09:41:20 CDT

Dear NAMD users,

I encounter a problem related to 2 OH of the phosphate group of
thymidine monophosphate (TMP), which are immediately forming a nearly
triangular structure when doing a minimization-equilibration of an
enzyme-TMP complex with NAMD2.6. The complex as well as TMP were
parametrized in Amber9 using antechamber, parmchk and tleap with FF99
and GAFF.

How could I avoid this "phosphate collapse" by:
a) Parametrizing TMP correctly in AMBER or
b) Restraining the distance between the 2 OH within NAMD?

Below I list the things I tried already for b):

- I modified and applied the following tcl script to the oxygen atoms
of the hydroxyls:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4984.html,
but obtained a failure in the RATTLE algorithm for an oxygen in one of
the 2 OH (still getting too close to each other). Perhaps, I did a
mistake in setting r0, so could you please recall me how to define it
correctly?

- Besides, I tried the extraBond feature in NAMD2.7b1, but got the
following error: Fatal error on PE 0> FATAL ERROR: BAD LINE IN EXTRA
BONDS FILE extrabonds.txt: bond [5040] [5042] [7.0] [2.43]. I guess
this is because my solvated_complex.pdb generated with tleap in Amber9
does not have the same numbering as the NAMD atom indices scheme. Is
there any known workaround?

Thank you very much in advance.

Best regards,

Yvonne Westermaier

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