[gmx-users] Automated Topology Builder changes randomly name of molecule submited

Dallas Warren dallas.warren at monash.edu
Mon Nov 4 19:22:24 CET 2019


ATB creates its own residue names, with a unique code. If you want
something else, just rename it once you get the files back.

With the atom types, as it says on the ATB site, ff 53a7_atb has some
unique atom types, so you have to use the force field files provided, which
do contain those atom types and interactions. For you do that?

On Mon, 4 Nov. 2019, 7:44 am daniel depope, <nevjernik at gmail.com> wrote:

> Hello
>
> I want to create gromos54a7 topology for pope.pdb lipid molecule on ATB
> website.
> I tried two times: resulting pope.itp file  gives random name of residue:
> ZH3J or KSPK (instead od POPE or eventually POP).
> Additionally, some unknown atomtypes appears such as: CPos, OEOpt, or OAlc
> which gromacs doesn't recognize.
>
> Any advice what's going on here?
>
> Thanks
>
> Daniel
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