Thank you for your suggestion but I found a different solution.
Namely
set default reorder_residues off
in tleap.in turns off the default reordering.
Best wishes,
Dawid
czw., 10 paź 2019 o 16:47 Bill Ross <ross.cgl.ucsf.edu> napisał(a):
> I'd find the leap src dir, go there, and
>
> $ grep -i saveamberparm *.c
>
> I vaguely recall sorting molecules at the beginning.
>
> It looks like CP2K only uses the topology from prmtop, though if it's
> used to prmtop's, ions after water might confuse it, since it will never
> have seen that order.
>
> https://www.cp2k.org/exercises:2017_ethz_mmm:c2h2_bond_energy?s[]=amber
>
> Bill
>
> On 10/10/19 7:36 AM, Dawid das wrote:
> > I need the tleap only for generating parm. I will use it as an input for
> > CP2K. Then the trajectory in CP2K
> > is used further by me and it is important for me that the atoms have the
> > same order in every step
> > of my project.
> >
> > So I guess, that this ordering is hard-coded, right? If so, what source
> > files should I change to get rid of that?
> >
> > Best wishes,
> > DG
> >
> > czw., 10 paź 2019 o 16:13 Bill Ross <ross.cgl.ucsf.edu> napisał(a):
> >
> >> Is the order in the file more important than running at optimal speed?
> >> Solute atoms go before solvent atoms for the convenience of the solvent
> >> optimizations. I suggest you just reorder PDB's before using them for
> >> whatever is so vital.
> >>
> >> Bill
> >>
> >> On 10/10/19 7:09 AM, Dawid das wrote:
> >>> Dear Amber Users,
> >>>
> >>> I struggle with one more problem. Namely in my PDB file, the order
> >>> of units is the following:
> >>>
> >>> protein
> >>> water
> >>> ions (Na+, Cl-)
> >>>
> >>> But saveAmberParam yields *parm and *rtp files with the following order
> >>>
> >>> protein
> >>> ions (Na+, Cl-)
> >>> water
> >>>
> >>> I tried to change the order of loading libraries for ions and solvents
> >> but
> >>> it doesn't work. It's really important for me to conserve the order
> from
> >>> PDB file. How could I do it?
> >>>
> >>> Best regards,
> >>> Dawid Grabarek
> >>>
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Received on Thu Oct 10 2019 - 08:30:03 PDT
