[AMBER] problem with heme parameters bound to HIS

From: <moitrayee.mbu.iisc.ernet.in>
Date: Fri, 18 Oct 2013 14:35:48 +0530 (IST)

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


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.

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,

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
AMBER mailing list
Received on Fri Oct 18 2013 - 02:00:06 PDT
Custom Search