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
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:
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
- 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   [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.
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