add space here:
-o pdb_wat_md1.out-p
--> -o pdb_wat_md1.out -p
Hai
On Wed, Nov 30, 2016 at 6:32 PM, Aishani Prem <aishaniprem.gmail.com> wrote:
> 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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>
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Received on Wed Nov 30 2016 - 16:00:03 PST
