Dear Amber user,
I am new to Amber. I am using Amber8 and wanted to simulate a protein with 5 calcium ions as regulator.
I am referring to this thread in Amber Archive (
http://structbio.vanderbilt.edu/archives/amber-archive/2007/3730.php) and simple tutorial of A1
When I tried to declare bonds between calcium ions and residues, I got this argument
Sourcing: /usr/local/amber8/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber8/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber8/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber8/dat/leap/lib/solvents.lib
> loadoff Ca2draw.lib
Loading library: ./Ca2draw.lib
> 1WD9 = loadpdb 1WD9_Ca2.pdb
Loading PDB file: ./1WD9_Ca2.pdb
Leap added 5315 missing atoms according to residue templates:
5315 H / lone pairs
> bond 1WD9.349.OE1 1WD9.900.Ca
bond: Argument #2 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1WD9.353.OE1 1WD9.900.Ca
bond: Argument #2 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
1) I would be grateful if anyone can tell me how to assign the bonds correctly. Is the command wrong?
2) I couldnt find frcmod.ff99SB file (it may due to the use of Amber8, this is all I have). Can I just use ff99?
Thanks in advance for the help and suggestion
Zalikha Ibrahim
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Received on Tue Jul 17 2012 - 01:30:02 PDT
