Well it depends how the OP has set up their simulation. Was trying to
help. :) What you're saying is right of course.
On 2 July 2016 at 21:45, Justin Lemkul wrote:
>
>
> On 7/1/16 9:51 PM, Billy Williams-Noonan wrote:
>
>> Hi Justin,
>>
>> I've found that I get this error with my relative FE
On 7/1/16 9:51 PM, Billy Williams-Noonan wrote:
Hi Justin,
I've found that I get this error with my relative FEP calculations if my
.gro file with the relevant protein and ligand coordinates, describes the
protein numbering from a1-3017, and the ligand from 3018 onwards for
example, while in m
Hi Justin,
I've found that I get this error with my relative FEP calculations if my
.gro file with the relevant protein and ligand coordinates, describes the
protein numbering from a1-3017, and the ligand from 3018 onwards for
example, while in my topology file, a1-3017 refer to the same protein,
On 6/30/16 11:22 PM, Billy Williams-Noonan wrote:
Hi Thanh,
Maybe try to check if the numbering of your atoms in the topology files is
consistent with the .pdb or .gro files they describe.
Coordinate file and topology file numbering are different and use different
conventions. In fact, if
Hi Thanh,
Maybe try to check if the numbering of your atoms in the topology files is
consistent with the .pdb or .gro files they describe.
Billy
On 1 July 2016 at 09:20, Thanh Le wrote:
>
> > On Jun 30, 2016, at 3:48 PM, Thanh Le wrote:
> >
> > My name is Thanh Le, a graduate student in chemi
> On Jun 30, 2016, at 3:48 PM, Thanh Le wrote:
>
> My name is Thanh Le, a graduate student in chemistry. Currently, I am using
> gromacs to do a dynamics simulation for my RNA-protein complex. I saw you
> posted a question titled “Atoms in the .top are not numbered consecutively
> from 1” on
