On Fri, Oct 18, 2013, moitrayee.mbu.iisc.ernet.in wrote:
>
> # my leap input file:
>
> loadamberparams frcmod.hemuni
> loadamberprep heme_uni.in
> addAtomTypes { { "DZ" "Zn" "sp3" } { "Zn" "Zn" "sp3" } }
> loadOff znb.lib
> loadOff hin.lib
> loadOff hydroxide.lib
> loadamberparams frcmod.zinc
It doesn't look like have loaded any libraries for HID.
> fep = loadpdb clnFePPIX-noH.pdb
> addions fep Na+ 0
> solvatebox fep TIP3PBOX 10.00 0.75
> saveamberparm fep fep.prm.top fep.prm.crd
> quit
>
> Error:
>
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 181>.A<CA 3> Could not find type: CH
> For atom: .R<HEM 181>.A<CB 4> Could not find type: C2
> For atom: .R<HEM 181>.A<CE1 8> Could not find type: CP
> For atom: .R<HEM 181>.A<CD2 10> Could not find type: CF
> For atom: .R<HEM 181>.A<FE 11> Could not find type: FE
> For atom: .R<HEM 181>.A<CAA 15> Could not find type: C2
> For atom: .R<HEM 181>.A<CBA 16> Could not find type: C2
> For atom: .R<HEM 181>.A<CAD 49> Could not find type: C2
> For atom: .R<HEM 181>.A<CBD 50> Could not find type: C2
These errors indicate that the atom types in the heme_uni.in file don't match
those in the frcmod files you have used. You will have to check the files
themselves: I doubt that anyone has tried to use united atom simulations for
porphyrins in several decades.
....dac
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Received on Fri Oct 18 2013 - 08:30:05 PDT
