Hi All,
I'm a bit confused and not really sure what is going on.
Using
AmberTools version 14.12
Amber version 14.06
I'm trying to simulate a POPC/Cholesterol/protein system.
My understanding was that any parm missing from lipid14 could be used
by loading the lipid14_supp.lib.
However, Cholesterol (CHL) param can't be generated. Specifically,
leap kicks out the error that it can't find and vdW parameters for H
or O.
for example:
For atom: .R<CHL 352>.A<H11 2> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H12 3> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H21 5> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H22 6> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H41 10> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H42 11> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H71 16> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H72 17> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H81 19> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H91 21> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H111 24> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H112 25> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H121 27> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H122 28> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H141 31> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H151 33> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H152 34> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H161 36> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H162 37> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H171 39> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H181 41> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H182 42> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H183 43> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H191 45> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H192 46> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H193 47> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H201 49> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H211 51> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H212 52> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H213 53> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H221 55> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H222 56> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H231 58> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H232 59> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H241 61> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H242 62> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H251 64> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H261 66> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H262 67> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H263 68> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H271 70> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H272 71> Could not find vdW (or other)
parameters for type: hA
For atom: .R<CHL 352>.A<H273 72> Could not find vdW (or other)
parameters for type: hA
leap can build CHL and the appropriate .lib .prmtop .inpcrd using lipid11.
Even if I load the CHL.lib created with lipid11 (via leap) I can't use
it with lipid14 parm (I get the same vdW errors). I'm really
confused...
comparing the lipid11.lib and lipid14_supp.lib I can't seem to find
any difference between the 2 CHL entries (via diff).
any insight or help would be greatly appreciated.
Thanks,
Jonathan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 21 2014 - 10:30:02 PST
