On 11/04/2011 23:40, Jason Swails wrote:
> Hello everyone,
> %FLAG SOLVENT_POINTERS
> %FORMAT(3I8)
> 6 1081 3
> %FLAG ATOMS_PER_MOLECULE
> %FORMAT(10I8)
> 22 33 3 3 3 3 3 3
> 3 3
>
> Here, ACE-ALA-NME and ACE-TYR-NME are separate molecules. (the 1113 vs.
> 1081 just shows that tleap packed a couple more water molecules inside... no
> big deal). I think this is probably an issue that should be resolved prior
> to the release of AT 1.5.
Hi Jason,
I recall difficulties of a similar nature when dealing with the
conversion of PBC systems in chamber . I hit many issues when
calculating SOLVENT_POINTERS and ATOMS_PER_MOLECULE since the needed
information from the charmm input, MOLNT and iMOLNT, were not always
guaranteed to be present.
In the end, I wrote a set of routines that could determine molecular
topology in a system solely from the bonded list. These are found in the
molnt module in AmberTools/src/chamber/molnt.f . I don't know too much
about sleap, but maybe this algorithm could be applied just before sleap
writes a prmtop? I recall it being pretty robust.
Regards,
Mark
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Received on Mon Apr 11 2011 - 16:30:03 PDT
