Dear Amber Users,
I am trying to run an MD for a protein with a heme that is pentacoordinated with
His (delta protonated; i have renamed this his as HID). I downloaded the united
atom force field from the contributed parameters site. However, I run into
errors as follows:
# 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
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
Parameter file was not saved.
Quit
I believe this is due to the fact that it does not recognize the HID as part of
the HEM force fileld.
I would look forward towards any suggestions for this problem.
Thanks a lot in advance.
Best Regards,
Moitrayee
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Received on Fri Oct 18 2013 - 02:00:06 PDT
