> 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
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Received on Wed Jun 14 2017 - 13:30:03 PDT
