Dear amber users
I was trying to do md simulationon a small peptide using amoeba force filed in amber 10. I am getting the error message . Spline order too small. Must be at least 5.Would please help me in fixing this problem. I have listed the steps I followed
I created the coordinate and topology file using
sleap
source leaprc.amoeba
COM = loadpdb Peptide.pdb
saveamoebaparm COM Peptide.prmtop Peptide.inpcrd
then I used minimization in implicit solvent
fname_min.in
initial minimisation prior to MD GB model
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 2
iamoeba = 1, jfastw=4,
cut = 12, tautp=5.0,
/
&ewald
nfft1=80,nfft2=80,nfft3=80,
skinnb=2.,nbtell=0,order=5,ew_coeff=0.45,
/
&amoeba
do_bond=1,do_ureyb=1,do_reg_angle=1,do_trig_angle=1,
do_opbend=1,do_torsion=1,do_pi_torsion=1,do_strbend=1,
do_torsion_torsion=1,do_amoeba_nonbond=1,
dipole_scf_tol = 0.01,dipole_scf_iter_max=20,
sor_coefficient=0.7,ee_damped_cut=4.5,ee_dsum_cut=6.7,
amoeba_verbose=1
/
$AMBERHOME/bin/sander -i Fname_min.in -o Peptide_min.out -c Peptide.inpcrd -p Peptide.prmtop -r Peptide_min.rst -ref Peptide.inpcrd
The error message is
Spline order too small. Must be at least 5
Could please give me a your adivse omn what is wrong with what I am doing and how to fix it.
I also tried to do it in explicit solvent
I used
sleap
source leaprc.amoeba
COM = loadpdb Peptide.pdb
charge COM
solvateoct COM TIP3PBOX 10.
saveamoebaparm COM Peptide.prmtop Peptide.inpcrd
I am getting the error
sleap: solvate.cpp:30: virtual bool amber::solvate_command::exec(): Assertion `p solute != __null && psolvent != __null' failed.
Abort
Could you also please help in find a solution to this problem too
Thank you
With best regards
Workalemahu
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Received on Sat Mar 13 2010 - 05:00:02 PST
