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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 06 2016 - 09:30:02 PDT
