VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 04 2011 - 19:31:24 CDT

Hi Francesco,
Could you send me the structure that you're working on and tell me the
exact set of steps that you followed? I'm glad that things work when you
add hydrogens in chimera, but this is really a suboptimal solution --
molefacture should be able to handle this on its own.
Thanks,
Peter

On 05/04/2011 02:33 AM, Francesco Pietra wrote:
> Hello:
> i am trying to add the non-polar hydrogens to a marine metabolite pdb.
>
> Problems in adding H to bare methyl groups, be them at a methyl ester
> chain C(O)-O-C or at isopropyl group -CHCC. The umbrella of the three
> hydrogens added to C (C(O)-O-CH3) is built toward the oxygen atom. As
> to the i-prop, -CH(CH3)(CH3) one of the two methyls comes out correct,
> the other one with inverted umbrella, as described for the methyl
> ester.
>
> H addition follows the spatial direction of the initial violet
> elongations: if this is incorrect, i found no way to remedy it. "force
> tetrahedral" (in order to invert the umbrella), while picking on
> either the methyl carbon, or the latter plus the three hydrogen atoms,
> or at any intermediate stage of the H addition, does not move
> anything.
>
> I could replace the three H with different groups, for example H, F,
> D, in order to use "invert chirality" but there should be something
> simpler and I am simply misusing molefacture. Or this is a situation
> that deceits molefacture.
>
> thanks for advice
> francesco pietra