Steve,
> I have been attempting to load the pdb file which, as you can see in
> the attachment is identical in residues, atom names to the mol2
> file and still I am getting the error in leap saying it does not
> have atom types for my pdb. I have also attempted with "TER" and in
> its absence to no success.
The residue name & atom names have to be identical in the PDB and mol2 files.
Thus, this is normal it does not work.
The residue names in the mol2 file are: P2M P1 P1 & C5
The residue names in the PDB file are: PM2 P1 P1 & C5
Moreover, there are errors in the residue name (shift & empty character).
Check also for putative inversion in atom names (for instance H11
which becomes 1H1).
> I hope I am not doing something dumb and wasting your time. I am
> sending you everything I am using. Can you give it a glance and tell
> me if you have any ideas?
See above & below.
> Is the problem that these mol2 files were not made with gaff.dat/antechamber?
> Is there a way to convert mol2 files to prepi files if necessary or
> would this even help?
I think this is a general problem of FF library recognition.
regards, Francois
Below is wrong:
REMARK
HETATM10305 OR PM2 A 201 46.999 35.394-110.730 1.00 32.71 O
HETATM10306 P PM2 A 201 48.402 34.814-111.258 1.00 32.34 P
HETATM10307 OP1 PM2 A 201 48.870 33.764-110.316 1.00 33.57 O
HETATM10308 OP2 PM2 A 201 48.292 34.479-112.691 1.00 33.25 O
TER
HETATM10309 OP3 PM2 A 202 49.362 36.087-111.126 1.00 32.50 O
HETATM10301 OR P1 A 202 44.930 34.458-111.161 1.00 29.92 O
HETATM10302 P P1 A 202 45.783 35.734-111.732 1.00 31.42 P
HETATM10303 OP1 P1 A 202 44.906 36.821-111.230 1.00 30.92 O
HETATM10304 OP2 A 202 45.895 35.340-113.143 1.00 32.96 O
etc...
It should be as in the mol2 file, i. e.:
REMARK
HETATM10305 OR P2M A 201 46.999 35.394-110.730 1.00 32.71 O
HETATM10306 P P2M A 201 48.402 34.814-111.258 1.00 32.34 P
HETATM10307 OP1 P2M A 201 48.870 33.764-110.316 1.00 33.57 O
HETATM10308 OP2 P2M A 201 48.292 34.479-112.691 1.00 33.25 O
HETATM10309 OP3 P2M A 201 49.362 36.087-111.126 1.00 32.50 O
TER
HETATM10301 OR P1 A 202 44.930 34.458-111.161 1.00 29.92 O
HETATM10302 P P1 A 202 45.783 35.734-111.732 1.00 31.42 P
HETATM10303 OP1 P1 A 202 44.906 36.821-111.230 1.00 30.92 O
HETATM10304 OP2 P1 A 202 45.895 35.340-113.143 1.00 32.96 O
etc...
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Received on Thu Sep 17 2009 - 09:30:01 PDT
