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| 2:19:23 AM PDT - Mon, Jun 9th 2014 |
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Hello,
I tried to compute a QMMM calculation from a pdb file. First of all, I want to create the topology and restart file using the prepare module. I read the documentation about the preparation of this file but I do not understand what im doing wrong...
Here is my PDB file :
ATOM 1 1C0 RE1 1 8.779 4.095 0.000 1.00 0.00 C
ATOM 3 1C2 RE1 1 2.925 0.000 0.000 1.00 0.00 C
ATOM 4 1C3 RE1 1 2.925 8.189 0.000 1.00 0.00 C
ATOM 5 1C4 RE1 1 2.925 0.000 8.184 1.00 0.00 C
ATOM 6 1C5 RE1 1 2.925 8.189 8.184 1.00 0.00 C
...
ATOM 2 1C1 RE2 2 8.779 4.095 8.184 1.00 0.00 C
ATOM 19 1H0 RE2 2 9.378 4.746 7.641 1.00 0.00 H
ATOM 39 3H0 RE2 2 8.179 3.552 7.533 1.00 0.00 H
ATOM 105 8H4 RE2 2 9.378 3.443 8.727 1.00 0.00 H
ATOM 106 8H5 RE2 2 8.179 4.638 8.836 1.00 0.00 H
My input file is :
title "QMMM cell"
echo
start qmmm_cell
prepare
source cell1.pdb
new_top new_seq
new_rst
#define quantum region residue:name
#modify atom 2:1C1 quantum
#modify atom 2:1H0 quantum
#modify atom 2:3H0 quantum
#modify atom 2:8H4 quantum
#modify atom 2:8H5 quantum
modify segment 2 quantum
update lists
ignore
write cell.rst
write qmmm.pdb
end
Unfortunetly, the qmmm.pdb file does not want to be created and I have this output file:
...
Coordinates missing for atom 1:RE1 H7
Coordinates missing for atom 1:RE1 H8
Coordinates missing for atom 1:RE1 H9
Coordinates missing for atom 1:RE1 H0
Coordinates missing for atom 1:RE1 H1
Coordinates missing for atom 1:RE1 H6
Coordinates missing for atom 1:RE1 H7
Coordinates missing for atom 1:RE1 H8
Coordinates missing for atom 1:RE1 H5
Coordinates missing for atom 1:RE1 H6
Coordinates missing for atom 1:RE1 H7
Added counterion with energy 0.000 kJ/mol
Grid specifications for non-bonded atoms done
**********
* 0: pre_misfit: missing non hydrogen coordinates 9999
You can remark that I fixed 2 different residual name. The first one is the MM region and the second is the QM region that I want to define in the prepare module.
When I define the QM region atom per atom with the commented command, I obtain another output :
modify atom 2:1C1 set 0 quantum
**********
* 0: Atom not found for quantum 0
What I am doing wrong? How can I define QM and MM region in the input file?
Thank you in advance!
Guillaume
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