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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Received on Tue Oct 01 2024 - 09:30:03 PDT
