Thanks. I am changing all the atom names manually. Meanwhile I just
saved the mol2 file generated from the project F-90 as PDB and loaded in
tleap alongwith the .off file (over ff99SB). Upon checking I find
missing angle parameters.
Checking for angle parameters.
Could not find angle parameter: NC - CB - CA
Could not find angle parameter: CB - NC - CB
Could not find angle parameter: CB - N* - CB
Could not find angle parameter: N* - CB - CA
Could not find angle parameter: C - CB - NC
Could not find angle parameter: C - NC - CB
Could not find angle parameter: NC - C - NA
Am I doing something wrong here?
Amin.
On 2014-05-02 00:50, Jason Swails wrote:
> On Fri, 2014-05-02 at 00:35 +0530, amin.imtech.res.inwrote:
> Thanks. I downloaded the project files and generated the mol2 and .off files. I loaded the .off file using loadoff. Now I can see FAD in the list. But when I load the pdb file of FAD, i get fad = loadpdb FAD.pdb Loading PDB file: ./FAD.pdb Created a new atom named: P within residue: .R<B5 904> Created a new atom named: PA within residue: .R<B5 904>
[snip]
> Created a new atom named: N10 within residue: .R<B5 904> Added missing heavy atom: .R<B5 904>.A<N9 25> Added missing heavy atom: .R<POP 905>.A<O5A 1> Added missing heavy atom: .R<POP 905>.A<PA 2> Added missing heavy atom: .R<POP 905>.A<OA1 3> Added missing heavy atom: .R<POP 905>.A<OA2 4> Added missing heavy atom: .R<POP 905>.A<OP 5>
[snip]
> Added missing heavy atom: .R<B5 904>.A<N6 17> Added missing heavy atom: .R<B5 904>.A<N7 22> total atoms in file: 53
All of the atom names from the residue in FAD.pdb _must_ match the atom
names used for the same atoms in the OFF files you downloaded.
That's how leap is able to determine the appropriate atom types. You
will need to modify all of the atom names in the FAD residue in your PDB
file to match those stored in the OFF files.
HTH,
Jason
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Received on Thu May 01 2014 - 22:30:02 PDT
