Based on the output you posted, you quit before you actually wrote the
topology file. You need a ‘saveamberparm’ command after you add your ions.
-Dan
On Tue, Oct 1, 2019 at 11:34 AM Parviz Seifpanahi Shabane <sparviz.vt.edu>
wrote:
> Hi All,
> I created a system and added ions. Used Na+ for neutralizing the system and
> K+ and Cl- to add 0.2 M salt. This part of my script:
> saveamberparm mol F1KX5-iodFF-KCLNa-SLTCAP-Acy.top
> F1KX5-iodFF-KCLNa-SLTCAP-Acy.crd
>
> addIonsRand mol K+ 453
> addIonsRand mol Na+ 147
> addIonsRand mol Cl- 453
> I used "addIonsRand" as I have too many ions to add. This what I have in
> log file:
> > addIonsRand mol K+ 453
> Adding 453 counter ions to "mol". 152781 solvent molecules will remain.
> 0: Placed K+ in mol at (-66.56, 16.55, 12.03).
> 0: Placed K+ in mol at (-73.03, -95.38, -46.48).
> 0: Placed K+ in mol at (52.97, -96.86, -45.80).
> 0: Placed K+ in mol at (-50.79, 36.63, -55.77).
> 0: Placed K+ in mol at (76.68, -70.50, 52.14).
> ...
> > addIonsRand mol Na+ 147
> Adding 147 counter ions to "mol". 152634 solvent molecules will remain.
> 0: Placed Na+ in mol at (-24.82, 22.57, -33.85).
> 0: Placed Na+ in mol at (34.01, -28.88, 37.83).
> 0: Placed Na+ in mol at (57.46, -67.19, -57.17).
> 0: Placed Na+ in mol at (-45.51, 82.97, 8.61).
> 0: Placed Na+ in mol at (71.18, 65.50, -28.67).
> 0: Placed Na+ in mol at (-14.53, 89.80, -37.49).
> 0: Placed Na+ in mol at (-83.40, -75.44, -24.27).
> .....
> > addIonsRand mol Cl- 453
> Adding 453 counter ions to "mol". 152181 solvent molecules will remain.
> 0: Placed Cl- in mol at (28.68, 101.85, -54.61).
> 0: Placed Cl- in mol at (31.12, 2.09, 45.68).
> 0: Placed Cl- in mol at (88.16, -21.58, 57.79).
> 0: Placed Cl- in mol at (-10.34, -77.87, -48.98).
> 0: Placed Cl- in mol at (-29.82, -66.84, -12.28).
> 0: Placed Cl- in mol at (76.22, -23.47, 13.07).
> .....
> > quit
> Quit
>
> Exiting LEaP: Errors = 0; Warnings = 1761; Notes = 1.
> ================================================
> Probelm is when I make PDB file fron file.crd and file.top by "ambpdb"
> command I can not see any ions when I look at thesysteam by pymol or
> VMD!!!!
> what is the probelm?
> --
> Parviz Seifpanahi
> Ph.D. Candidate
> Department of Physics
> Virginia Tech, Blacksburg, Va 24061
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>
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Received on Tue Oct 01 2019 - 10:30:03 PDT
