Hi Dave,
On 13/8/2010, at 3:51 p.m., case wrote:
> We will need to know real details: what library did you use for the metal
> cluster? exactly what commands did you give to tleap?
The set of files I used, and the commands I sent to tleap, are kind of complex, so I didn't want to send it to the list in the first instance. Perhaps a bad call.
>>
>> The first is that both sleap and tleap seem to create spurious bonds
>> between the two nickel ions, which are far enough apart (3.5 to 4 Ã )
>> that they shouldn't be bonded to each other. I've checked the file, and
>> there are no CONECT records indicating that the two should be bonded.
>
> How do you know that tleap actually created the bonds? Did you use desc or
> rdparm? Unless you use something like "bondbydistance", tleap won't make
> bonds between atoms (again, unless those bonds are in some library file).
Well, tleap must have gotten them from somewhere, because they weren't in the original PDB. While for other reasons tleap refused to create a prmtop file, I got warnings about long bonds.
These are the actual tleap commands I performed (read from a file using tleap -f, which file sources other files):
source leaprc.ff99SB
source leaprc.gaff
urea_params = loadAmberParams URE.frcmod
loadOff cterm94mod.lib
loadOff nterm94mod.lib
loadAmberPrep URE.prepi
addAtomTypes {
{ "HX" "H" "sp3" }
{ "HQ" "H" "sp3" }
{ "N5" "Ni" "sp3" }
{ "N6" "Ni" "sp3" }
{ "NU" "N" "sp2" }
{ "NV" "N" "sp2" }
{ "NW" "N" "sp2" }
{ "NX" "N" "sp2" }
{ "OB" "O" "sp2" }
{ "OK" "O" "sp2" }
{ "OL" "O" "sp2" }
{ "ON" "O" "sp3" }
{ "OO" "O" "sp3" }
{ "OQ" "O" "sp3" }
{ "OU" "O" "sp2" }
}
frcmodMetals = loadamberparams metals.frcmod
frcmod = loadamberparams 1FWJ_high.frcmod
loadamberprep 1FWJ_chg2.prep
model = loadpdb BPR-20100812-002_mod.pdb
saveamberparm model BPR-20100812-002_out.parm7 BPR-20100812-002_out.rst7
savePdb model BPR-20100812-002_out.pdb
quit
I hope that helps a bit. I'm happy to supply more info. I was loath to send the PDB file straightaway, it being a 3 MB file.
Cheers,
Ben
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Received on Fri Aug 13 2010 - 13:30:20 PDT
