[gmx-users] fatal error

[Mark Abraham]

Hi,

pdb2gmx isn't magic. You have to to choose a force field that has an .rtp
file that has residue definitions that match what's in your coordinate
file. We currently can't know at which stage of this process the problem
is. :-)

Mark

On Mon, Mar 6, 2017 at 4:23 PM Urszula Uciechowska <
urszula.uciechowska at biotech.ug.edu.pl> wrote:

>
> Hi,
>
> I do not know. After running pdb2gmx I am not getting the .itp file for
> the DC5... I am using gromacs 5.0.4. What can be wrong here?
>
> Urszula
>
> > Hi,
> >
> > What name does the .rtp entry for DC5 use for its phosphorus atom?
> >
> > Mark
> >
> > On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska <
> > urszula.uciechowska at biotech.ug.edu.pl> wrote:
> >
> >> Dear gmx users,
> >>
> >> After running a pdb2gmx script of the pdb file I am getting an error
> >> message:
> >>
> >>
> >> Fatal error:
> >> Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms
> >> while sorting atoms.
> >>
> >>
> >> The DC 2 in pdb file:
> >>
> >> TER   11412      LEU B 366
> >> ATOM  11413  P   DC  C   2       0.997  17.702   5.368  1.00 77.21
> >>   P
> >> ATOM  11414  OP1 DC  C   2      -0.278  17.623   4.612  1.00 76.82
> >>   O
> >> ATOM  11415  OP2 DC  C   2       1.374  16.596   6.287  1.00 76.77
> >>   O
> >> ATOM  11416  O5' DC  C   2       2.181  17.899   4.319  1.00 75.66
> >>   O
> >> ATOM  11417  C5' DC  C   2       2.302  19.107   3.565  1.00 72.46
> >>   C
> >>
> >> What can be wrong with the P atom?
> >>
> >> Thanks for any suggestions.
> >>
> >> best
> >> Urszula Uciechowska
> >>
> >>
> >>
> >>
> >> -----------------------------------------
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> >> http://www.ug.edu.pl/
> >>
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>
> --------------------------------------------
> Urszula Uciechowska PhD
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Abrahama 58
> 80-307 Gdańsk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
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