On Tue, Nov 08, 2011, Jennifer Brookes wrote:
>
> I guess I do not understand the problem of duplicates in leap. From your
> email it seems that the residue number, res name and atom name (combination)
> must be unique.
>
> At the moment in my .pdb I have the atom numbers 1- 13440 (60x224), though
> each dimer of 224 atoms is separated by TER, resname LIG (for all dimers)
> and residue number 1 (again for all dimers). So for the combination of these
> three fields there should be no duplicates.
>
> I actually have never been able to load a .pdb file
What you have sounds fine. Can you either tell us what error messages you are
getting, or post the pdb file itself? As Carlos said, it sounds like you have
everything you need: in leap you would load the library and frcmod files for
the dimer, then use loadPdb to load the 60-mer pdb file, then saveamberparm
to save the prmtop file. If one of these steps is failing (e.g. the loadPdb
step) is failing, we need to see the exact error messages.
(Trying to use addles for this purpose is not going to work.)
....dac
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Received on Wed Nov 09 2011 - 07:30:04 PST
