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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Oct 10 2019 - 08:00:03 PDT
