Just a general comment.
The constant pH method, as implemented, has NOT been parametrized for
the ff19SB/OPC combination you are using.
If I were you, I would reparametrize the so-called reference energies.
Take a look at the manual on how to do that, using the findgref.py script.
Adrian
On 10/1/24 12:24 PM, Abdelrahman, Noureen via AMBER wrote:
> [External Email]
>
> Dear all,
>
> I used the following tleap code to generate smURFP parm7 and rst7 files:
>
> source leaprc.protein.ff19SB
> source leaprc.water.opc
> source leaprc.constph
> loadAmberPrep JRA.prepin
> loadAmberParams frcmod2_HN.JRA
> loadAmberParams frcmod1_HN.JRA
> x = loadPDB JRA.pdb
> bond x.51.SG x.266.CAB
> addions x Na+ 0.0
> addions x Cl- 0.0
> solvatebox x OPCBOX 12.0
> setbox x vdw
> savepdb x smURFP_pH.pdb
> saveAmberParm x smURFP_pH.parm7 smURFP_pH.rst7
> quit
>
> Now, I need to run pH REMD. To do that, I must create a new prmtop file with cpinutil.py and use the new intrinsic radii. When I do the following code:
>
> cpinutil.py -p smURFP_pH.parm7 -o smURFP_BV.cpin -op smURFP_BV_cpin.parm7 -resnames AS4 GL4 HIP LYS TYR CYS
>
> I get a warning message:
> AmberWarning: Molecule atoms are not contiguous!
>
> The created prmtop file (smURFP_BV_cpin.parm7) is incorrect because the protein bonds are stretched everywhere, and I cannot run classical MD using it. When I do, I get a LINMIN error at minimization.
>
> Has anyone encountered this before? Or does anyone know a fix? I cannot attach the prmtop and rst7 files because they're large but I attached all the files needed to reproduce them using tleap.
>
> Thanks,
> Noureen
>
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--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Oct 01 2024 - 10:30:02 PDT
