On Fri, Aug 06, 2004, tarek mahfouz wrote:
>
> I'm a new user of AMBER and I'm trying to run the plastocyanin tutorial and
> here is what I did:
>
> 1- I prepared the required input files hicu.in and mem.in. However, since
> later on in the leap.in input file the call is for mem.lib and hicu.lib, I
> saved hicu.in as hicu.lib and mem.in as mem.lib. They were read ok.
I'm lost here: the leap.in file refers to "hicu.in" and "mem.in", not to any
lib files (as far as I can see)? Can you post exactly what is in your
leap.in file, (and where you got it)? Here is what I see on the web site:
addAtomTypes {
{"SM" "S" "sp3"}
}
loadamberparams frcmod.pcy
loadAmberPrep mem.in
loadAmberPrep hicu.in
plc = loadPdb 1plc.protein.pdb
bond plc.87.ND1 plc.37.CU
bond plc.84.SG plc.37.CU
bond plc.92.SD plc.37.CU
saveAmberParm plc prmtop.nowat prmcrd.nowat
In particular, you should see if you have the "addAtomTypes" command in your
input.
> and I'm concerned about the statement "residue lacking connect0/connect1"
> does it mean it will not save the N and C termini as charged?
Don't worry about this message, it really doesn't mean anything important.
....good luck...dac
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Received on Fri Aug 06 2004 - 20:53:00 PDT
