[gmx-users] ignoring -h atoms
erik.marklund at kemi.uu.se
Wed Feb 8 09:46:02 CET 2017
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.
> 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.???
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users