Your input says ntb=0, which means NO periodic boundary conditions. You
also set igb=8, which means implicit solvent.
So, as written, what you have is a system with waters (you said you have
them, I cannot tell from the input alone), but that outside of it has
implicit solvent, no periodic boundary conditions, no constant volume
and no constant pressure.
adrian
On 9/6/16 10:04 AM, Chase Zagorec-Marks wrote:
> Hi,
>
> I have been trying to run the attached heating file for the 3phy protein, but when I run the file it returns with an error saying that for iwrap=1 there must be a periodic box; however, I solvated the protein using the TIP3PBOX command, so I don’t know why this error keeps coming up. Is there a problem when I am trying to save off the prmtop and inpcrd files or the heating file, and if so is there a way that I can fix that issue?
>
> Thanks,
> Chase Zagorec-Marks
>
>
> Input File:
>
> Implicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=100000,
> dt=0.002, ntt=3, tempi=10,
> temp0=300, gamma_ln=1.0, ig=-1,
> ntp=0, ntc=2, ntf=2, cut=1000,
> ntb=0, igb=8,iwrap=1
> /
> &wt
> TYPE='TEMP0', ISTEP1=1, ISTEP2=100000,
> VALUE1=10.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
>
>
> Leap.log file from xleap:
>
> solvatebox x TIP3PBOX 8
> Solute vdw bounding box: 38.568 41.661 37.342
> Total bounding box for atom centers: 54.568 57.661 53.342
> Solvent unit box: 18.774 18.774 18.774
> … … … …
> … … … ...
> saveamberparm x 3phy_3_solvated_2.prmtop 3phy_3_solvated_2.incprd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -6.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2
> total 405 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CVAL 1
> HC4 1
> NMET 1
> WAT 4307
> )
> (no restraints)
>> quit
> Quit
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Sep 06 2016 - 09:30:02 PDT
