Re: [AMBER] tleap changes order of atoms in the parm file

From: Bill Ross <>
Date: Thu, 10 Oct 2019 11:48:34 -0700

Aha, it would have been discoverable from looking at the code as well. I might have even added it myself, now I hear of it.BillAI:
-------- Original message --------From: Dawid das <> Date: 10/10/19 8:14 AM (GMT-08:00) To: AMBER Mailing List <> Subject: Re: [AMBER] tleap changes order of atoms in the parm file Thank you for your suggestion but I found a different solution.Namelyset default reorder_residues offin turns off the default reordering.Best wishes,Dawidczw., 10 paź 2019 o 16:47 Bill Ross <> 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.>>[]=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 <> 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> >>>> >>> _______________________________________________> >>> AMBER mailing list> >>>> >>>> >> _______________________________________________> >> AMBER mailing list> >>> >>> >>> > _______________________________________________> > AMBER mailing list> >> >> >>> _______________________________________________> AMBER mailing list>>>_______________________________________________AMBER mailing listAMBER.ambermd.org
AMBER mailing list
Received on Thu Oct 10 2019 - 12:00:02 PDT
Custom Search