Hi all,
As a test, I used tleap to save .prmtop and .inpcrd files for RU3 (R-URACIL
- with 5' - phosphate group and 3' - OH group) based on ff99SB.
When I inspect the resulting .prmtop file with rdparm, I found the P
-O5'-C5'-H5'1 and P -O5'-C5'-C4' dihedral parameters were
0.383 0.00 3.0
But these two dihedrals have atom types as P -OS-CT-H1 and P -OS-CT-CT,
which should match X -CT-OS-X (1.15 0.0 3.0) in parm99.dat. And I found
this 0.383 force constant is from one term of a combination like
CT-CT-OS-CT/C/N* (0.383 0.0 -3.0) in parm99.dat. So is there something
wrong with my tleap?
I also found similar discrepancy for O1P-P -O5'-C5' (atom type: O2-P
-OS-CT), which was recognized as only the first term of OS/OH-P -OS-CT
(0.25 0.0 -3.0) in the prmtop file. But I assume it should use X -OS-P -X
(0.75 0.0 3.0).
Thanks for any suggestion,
Yun
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Received on Mon Jul 16 2012 - 10:30:03 PDT
