Hi,
I am trying to run simulations for a 56 residue protein in water but I
keep running into this error when I submit my job on the cluster.
cluster command -
$AMBERHOME/bin/sander -O -i pdb_wat_md1.in -o pdb_wat_md1.out-p
pdb_wat.prmtop -c pdb_wat_min2.rst -r pdb_wat_md1.rst -x pdb_wat_md1.mdcrd
-ref pdb_wat_min2.rst
mdin file-
MD with res on protein
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 1 56
END
END
Error-
mdfil: Error unknown flag:
pdb_wat.prmtop
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -frc mdfrc -idip
inpdip -rdip rstdip -mdip mddip
-inf mdinfo -radii radii -y inptraj -amd amd.log
-scaledMD scaledMD.log] -cph-data <file>
Can you tell me what went wrong. The topology file worked when I ran energy
minimization on the protein.
--
Thank You and Regards,
Aishani Chittoor Prem
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Received on Wed Nov 30 2016 - 16:00:02 PST
