Hi all,
Thanks to all those who responded regarding specifying improper
dihedrals manually. In the end, I've chosen to edit the prmtop by hand
(since I only have four impropers to add, and generating a DISANG file
seemed the more complicated of the two approaches).
So, I changed the MPHIA and NPHIA numbers at the top of the PRMTOP
file, and added the new dihedrals in the DIHEDRALS_WITHOUT_HYDROGEN
section of the PRMTOP. Specifically:
<snip>
34623 34647 -34620 -34611 43
%FLAG EXCLUDED_ATOMS_LIST
<snip>
becomes
<snip>
34623 34647 -34620 -34611 43 20088 20094 20091
-0 44
21228 21237 21234 -0 44 15294 15303 15300
-3 44
15402 15411 15408 -3 44
%FLAG EXCLUDED_ATOMS_LIST
<snip>
Which is all well and good, but when I ran "rdparm dihedrals" on this
file, it marked the new dihedrals - which is fine - but only the
second two showed up as impropers (i.e., with an I before them).
Output from rdparm:
<snip>
45137: 1.000 3.14 2.0 :448.CG :448.CE1 :448.ND1 :1.NI
(6697,6699,6698,1)
45138: 1.000 3.14 2.0 :474.CE1 :474.CD2 :474.NE2 :1.NI
(7077,7080,7079,1)
I 45139: 1.000 3.14 2.0 :336.CE1 :336.CD2 :336.NE2 :2.NI
(5099,5102,5101,2)
I 45140: 1.000 3.14 2.0 :338.CE1 :338.CD2 :338.NE2 :2.NI
(5135,5138,5137,2)
<snip>
Now I know that to specify an improper, one makes the fourth number
negative - as you can see I've done. But it looks to me as though,
because that fourth number is zero in this case, it's interpreted it
as a non-negative number!
Is there any way around this?
Cheers,
Ben
--
Benjamin P. Roberts
Postdoctoral Research Associate
Quantum Theory Project
University of Florida
2301 New Physics Building #92
PO Box 118435
Gainesville FL 32611-8435
USA
Phone: +1 352 392 6712
Cell: +1 352 222 3677
Member of the Royal Australian Chemical Institute
and of the American Chemical Society
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Received on Mon Jul 06 2009 - 09:54:46 PDT
