Hi Dr. Case,
Thanks a lot for your reply.
I realized from the previous amber forum emails as well as this one that using
the united ff for heme bound to His is not the most up-to-date approach. I am
also aware of the recent publications on heme ff bound to Cys in case of
cytochromes. However, in my system of interest I need a penta-coordinated Heme
with His bound to it. What according to you would be the best approach.
Thanks again for all your help on this.
Best Regards,
Moitrayee
> 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 - 09:30:03 PDT
