Ben, why don't you put the files on a web server and give the address so that people who may want to have a look at your problem have all infos at hand.
All the best,
Andy
On Aug 13, 2010, at 1:08 PM, Ben Roberts wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 13 2010 - 13:30:21 PDT
