Thanks! That appears to have been the problem, I fixed the input file and it
has been running for a while now.
Chase
> On Sep 6, 2016, at 10:07 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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 - 10:00:02 PDT
