Proffesor Swails,
You are right, this happen when I write the pdb file from its modified
parm7 and crd files, my system is 207571 atoms in 64343 residues. I will
check if both parm7 files agree for TMD simulation.
Thank you for your answer,
Greeting,
Hector.
>
>
>> On Jun 14, 2017, at 3:44 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
>> wrote:
>>
>> Dear amber user,
>>
>> In amber16+AmberTolls17, I am trying to delete extra water molecules
>> from
>> two topology (and its crd files) to make both system the same number of
>> atoms, following the previous post:
>> http://archive.ambermd.org/201205/0053.html
>>
>> I made:
>> ===========================
>> # Loaded topologies: B.parm7
>> loadRestrt B.inpcrd
>> strip :64329-64343
>> printPointers
>> outparm prmtop2B inpcrd2B
>> go
>> ===========================
>>
>> However, when residue number reach the 9999 and/or atom number reach the
>> 99999 value, parmed restart numbering from 0 value.
>>
>>> From visual inspection of the crd file and commands:
>> cpptraj -p prmtop2B -y inpcrd2B -x inpcrd2B_cpptraj.pdb
>> and
>> ambpdb -p prmtop2B < inpcrd2B > inpcrd2B_ambpdb.pdb
>>
>> How can I renumber sequentialy both parm7 and crd files ?
>
> I'm not sure what you mean. Prmtop and inpcrd files have implicit atom and
> residue ordering. That is, no atom or residue numbers are explicitly
> stored, so it's impossible to "restart" numbering.
>
> What you describe is the way that most amber programs tend to deal with
> atom and residue numbers that are too big to fit in the fixed size fields
> of a PDB file when writing a PDB file from a prmtop with too many
> atoms/residues.
>
> This is true of any prmtop/inpcrd combo.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Adjunto (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
-.First thinghs first, but not necesarily in that order.-
-.The theoretical approach these days can predict/show almost anything,
but the ultimate truth lies in the experiment.-
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 14 2017 - 14:00:03 PDT
