[gmx-users] ignoring -h atoms

Erik Marklund erik.marklund at kemi.uu.se
Wed Feb 8 09:46:02 CET 2017

Dear Maria,

I’m not saying that it never makes a difference for the topology generation, but it depends on the quality of your input structure. Justin and I both gave examples of why you might want to use it. When you do, -ignh ignores the hydrogens in the input pdb and uses the rtp to model new ones. I don’t understand why you say that the “ff its ignore it”.

As for what is most reliable, that again depends on the quality of the input structure. Pdb2gmx -ignh normally does a good job.

Kind regards,

> On 8 Feb 2017, at 07:20, maria khan <mariabiochemist1 at gmail.com> wrote:
> Dear ERIK..
> """..No. -ignh ignores the hydrogen atoms in the input structure, but uses
> the rtp file(s) to generate new hydrogens. This is useful, for example,
> when some hydrogens are missing in the pdb file. The structure and topology
> will therefore contain hydrogens in the end also with -ignh."""..
> now i have confusion if the ff ist ignore it and then in rtp files consider
> it..so why it at ist it ignores..there is no need to do so.after all h-atom
> will be same if it is in input file or when later form by rtp file.
> secondly what will be the consequences,,if in case it is ignored or not
> ignored..would it make difference to results in both cases.and if there
> would difference in results,,what kind of results are more reliable.???
> regards..
> -- 
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