Hello,
I have tried to set a QM/MM simulation using the prepare example given several years ago (http://nwchemgit.github.io/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...) and everything works fine. I try to use this example for my own system that has several pigment molecules (10 total = 8 peridinins + 2 chlorophyll a molecules) and somehow I am getting something wrong.
For example - here is my prepare file where I define the segments that I would like to simulate QM. The segments are all of the atoms of an individual pigment molecule:
prepare
- --name of the pdb file
source short_r.pdb
- --generate new topology and sequence file
new_top new_seq
- --use charmm forcefield
ffield amber
- --generate new restart file
new_rst
- --define quantum region
modify segment 313 quantum
modify segment 314 quantum
modify segment 315 quantum
modify segment 316 quantum
modify segment 317 quantum
modify segment 318 quantum
modify segment 319 quantum
modify segment 320 quantum
modify segment 321 quantum
modify segment 322 quantum
update lists
ignore
- --save restart file
write short_ref.rst
- --generate pdb file
write short_ref.pdb
After running prepare and modifying the fragment molecules of the two different molecules (an excerpt from one of them)
- This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 00/00/00 00:00:00
$LOP
96 1 1 0
LOP
1 H23 HQ 0 0 0 1 1 0.000000 0.000000
2 O2 OX 0 0 0 1 1 0.000000 0.000000
3 C3 CZ 0 0 0 1 1 0.000000 0.000000
4 H3 HQ 0 0 0 1 1 0.000000 0.000000
5 C2 CZ 0 0 0 1 1 0.000000 0.000000
6 H21 HQ 0 0 0 1 1 0.000000 0.000000
7 H22 HQ 0 0 0 1 1 0.000000 0.000000
8 C1 CZ 0 0 0 1 1 0.000000 0.000000
9 CM1 CZ 0 0 0 1 1 0.000000 0.000000
10 H8Q HQ 0 0 0 1 1 0.000000 0.000000
11 H8R HQ 0 0 0 1 1 0.000000 0.000000
12 HM1 HQ 0 0 0 1 1 0.000000 0.000000
13 C6 CZ 0 0 0 1 1 0.000000 0.000000
14 O1 OX 0 0 0 1 1 0.000000 0.000000
15 C5 CZ 0 0 0 1 1 0.000000 0.000000
16 C4 CZ 0 0 0 1 1 0.000000 0.000000
17 H41 HQ 0 0 0 1 1 0.000000 0.000000
18 H42 HQ 0 0 0 1 1 0.000000 0.000000
19 CM3 CZ 0 0 0 1 1 0.000000 0.000000
20 H8U HQ 0 0 0 1 1 0.000000 0.000000
21 H8V HQ 0 0 0 1 1 0.000000 0.000000
22 HM3 HQ 0 0 0 1 1 0.000000 0.000000
23 CM2 CZ 0 0 0 1 1 0.000000 0.000000
24 H8S HQ 0 0 0 1 1 0.000000 0.000000
25 H8T HQ 0 0 0 1 1 0.000000 0.000000
26 HM2 HQ 0 0 0 1 1 0.000000 0.000000
27 C7 CZ 0 1 0 1 1 0.000000 0.000000
28 H7 HQ 0 0 0 1 1 0.000000 0.000000
29 C8 CZ 0 1 0 1 1 0.000000 0.000000
30 H8 HQ 0 0 0 1 1 0.000000 0.000000
31 C9 CZ 0 1 0 1 1 0.000000 0.000000
32 C11 CZ 0 1 0 1 1 0.000000 0.000000
33 H11 HQ 0 0 0 1 1 0.000000 0.000000
34 C12 CZ 0 1 0 1 1 0.000000 0.000000
35 O4 OX 0 0 0 1 1 0.000000 0.000000
36 C10 CZ 0 1 0 1 1 0.000000 0.000000
37 O3 OX 0 0 0 1 1 0.000000 0.000000
38 C13 CZ 0 1 0 1 1 0.000000 0.000000
39 H13 HQ 0 0 0 1 1 0.000000 0.000000
40 C14 CZ 0 1 0 1 1 0.000000 0.000000
41 CM4 CZ 0 0 0 1 1 0.000000 0.000000
42 H8W HQ 0 0 0 1 1 0.000000 0.000000
43 H8X HQ 0 0 0 1 1 0.000000 0.000000
44 HM4 HQ 0 0 0 1 1 0.000000 0.000000
45 C15 CZ 0 1 0 1 1 0.000000 0.000000
46 H15 HQ 0 0 0 1 1 0.000000 0.000000
47 C16 CZ 0 1 0 1 1 0.000000 0.000000
48 H16 HQ 0 0 0 1 1 0.000000 0.000000
49 C17 CZ 0 1 0 1 1 0.000000 0.000000
and adding VdW amber parameters in my local amber.par file I still get the following error:
Parameter files used to resolve force field parameters
/usr/local/opt/nwchem/share/nwchem/amber_x/amber.par
/usr/local/opt/nwchem/share/nwchem/amber_u/amber.par
/usr/local/opt/nwchem/share/nwchem/amber_t/amber.par
/usr/local/opt/nwchem/share/nwchem/amber_s/amber.par
/usr/local/opt/nwchem/share/nwchem/amber_q/amber.par
./amber.par
Deleted existing sequence ./short.seq
PDB geometry short_r.pdb
Created sequence ./short.seq
modify segment 313 set 0 quantum
modify segment 314 set 0 quantum
modify segment 315 set 0 quantum
modify segment 316 set 0 quantum
modify segment 317 set 0 quantum
modify segment 318 set 0 quantum
modify segment 319 set 0 quantum
modify segment 320 set 0 quantum
modify segment 321 set 0 quantum
modify segment 322 set 0 quantum
Parameter file /usr/local/opt/nwchem/share/nwchem/amber_x/amber.par
Parameter file /usr/local/opt/nwchem/share/nwchem/amber_u/amber.par
Parameter file /usr/local/opt/nwchem/share/nwchem/amber_t/amber.par
Parameter file /usr/local/opt/nwchem/share/nwchem/amber_s/amber.par
Parameter file /usr/local/opt/nwchem/share/nwchem/amber_q/amber.par
Parameter file ./amber.par
Undetermined force field parameters
Parameters could not be found for atom type HQ Q
Parameters could not be found for atom type OX Q
Parameters could not be found for atom type CZ Q
Parameters could not be found for atom type NX Q
Parameters could not be found for atom type MG Q
**********
* 0: pre_check failed 9999
**********
0::Received an Error in Communication
If I use the same modified local amber.par file for the prepare example file everything works fine so I guess there is something fundamental about how one defines segments that I am missing?
Anyway, any help that anyone could possibly give me would be gratefully appreciated! I am not sure what else to try now.
Kristina
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