tutorial on plastocyanin

From: Ioana Cozmuta <ioana_at_nas.nasa.gov>
Date: Tue 1 Oct 2002 23:04:37 -0700 (PDT)


I am trying to run the tutorial on plastocyanin on an SGI octane station
with amber7.
I do have exactly the same modified files for HIS and MET (mem.in and
hicu.in) as shown on the tutorial web page. Also I generated a frcmod.pcy
forcefield correction file. Although I know that in amber7 the default
loaded force field is parm99, I did include in the input file the option
to load the parm94.dat file

Here is my input file to run with leap (the same almost as on the web

source leaprc.ff94
PARM94 = loadAmberParams frcmod.pcy
loadAmberPrep mem.in
loadAmberPrep hicu.lib
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

To run this I use exactly the command recommended in the tutorial
tleap -f leaprc.ff94
>parm94 = loadAmberParams parm94.dat
>source leap.in

I get the following error message in the leap.log file:
(after all that loading messages)
>> PARM94 = loadAmberParams frcmod.pcy
Loading parameters: ./frcmod.pcy
Reading force field mod type file (frcmod)
>> loadAmberPrep mem.in
Loading Prep file: ./mem.in
Unexpected EOF: discarding residue (STOP )

I looked into the parm94.dat file and indeed the SM atom type does not
exist so I changed it to SH in the mem.in file (BTW, I assume that the
files mem.lib and hicu.lib in the leap.in file from the tutorial web page
are actually mem.in and hicu.in generated previously). However parm94.dat
contains an atom type called CU so I do not understand why leap still does
not recognize it.

With this modification leap is running but there are some messages
that it spits out besides the UNKNOWN ATOM TYPE:CU that I would like to
understand if they are normal or not:
when loading the PDB file there is a long list of messages like the one
(Residue 1:ASP, Nonterminal, was not found in name map.)

then when generating the topology/Building improper torsion parameters
there is a long list of Warnings
**Warning: No sp2 improper torsion term for H-H-N3-H atoms are H1 H2 N H3

and then right in the end Residues lacking connect0/connect1 -these don't
have chain types marked

res total affected
(the last two are the C and N of the terminal residues so I assume it is
normal to have this message out).

The thing I am wondering mostly is why the CU atom type is not recognized
because this means also that the bonds specified in the leap.in file are
not made.

I hope this is not too messy so that someone could help me with some

Thank you,
Received on Tue Oct 01 2002 - 23:04:37 PDT
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