Comments (5)
Oh, FYI, it actually runs fine in Charmm. I'll change the issue name.
from htmd.
Process it through prepareProtein
and let me know if it solves it.
I think tleap
may be more picky than psfgen
regarding the capping.
Regarding AMBER, we're currently improving the integration to it, going through test phase.
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We mentioned this in another issue. Maybe we should add it to the documentation.
If you don't have hydrogens tleap cannot cap. Our only way of adding hydrogens before building right now is through prepareProtein
as Joao said.
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Noelia, I assume you built systems in the past with Amber. Do you remember how you added the caps? Because when I looked around the only solution that was mentioned around was replacing some atoms (one hydrogen and somethin else I think) from the terminal residues with an atom of the cap.
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Thanks guys. Passing it through prepareProtein solved it.
@stefdoerr yes that's the only option I think I knew of. Replacing the terminal atoms with one NME and ACE atoms respectively and tleap doing the rest.
i think I can close it.
thanks
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