| 5:07:13 AM PDT - Tue, Apr 23rd 2013 |
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Dear NWChem Developers and users,
I have met a little trouble during the running of the prepare module (used for QM/MM calculations).
In the preparation of the file fragment, I obtain the temporary frg, in which I have to associate the atom's label for the FF. But in this temporary file, there are some missed atoms. I did some tests and looks like that only the atoms with "M*" (such as Mg, Mn, Md, Mo) symbols give this problem. In the other tested cases, I obtained a correct temporary frg file.
As a result, I have to put at hand the atoms missing to carried out for my QM/ MM calculations. For smaller geometries this is not difficult but it can lead to errors for large structures.
Below, you can find my input and fragment file for a case in which there is the trouble. They are made by Charmm, but I have the same problem also by Amber.
Quote:INPUT
title "by charmm"
start mg
prepare
source mg.pdb
new_top
new_rst
charmm
modify atom 1:_S1 quantum
modify atom 1:_O1 quantum
modify atom 1:_O2 quantum
modify atom 1:_O3 quantum
modify atom 1:_S2 quantum
modify atom 1:_O4 quantum
modify atom 1:_O5 quantum
modify atom 1:_O6 quantum
modify atom 1:_MG1 quantum
update lists
ignore
write mg_ref.rst
end
task prepare
Quote:frg_TMP
- This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 04/22/13 18:12:38
$tst
16 1 1 0
tst
1 S1 0 0 0 1 1 -0.250000 0.000000
2 O1 0 0 0 1 1 -0.250000 0.000000
3 O2 0 0 0 1 1 -0.250000 0.000000
4 O3 0 0 0 1 1 -0.250000 0.000000
5 S2 0 0 0 1 1 -0.250000 0.000000
6 O4 0 0 0 1 1 -0.250000 0.000000
7 O5 0 0 0 1 1 -0.250000 0.000000
8 O6 0 0 0 1 1 -0.250000 0.000000
9 C1 0 0 0 1 1 0.000000 0.000000
10 H1 0 0 0 1 1 0.000000 0.000000
11 H2 0 0 0 1 1 0.000000 0.000000
12 H3 0 0 0 1 1 0.000000 0.000000
13 C2 0 0 0 1 1 0.000000 0.000000
14 H4 0 0 0 1 1 0.000000 0.000000
15 H5 0 0 0 1 1 0.000000 0.000000
16 H6 0 0 0 1 1 0.000000 0.000000
1 2
1 3
1 4
1 10
5 6
5 7
5 8
5 14
10 11
10 12
10 13
14 15
14 16
How you can see, in this case, the Magnesium is missed, In the Calcium case, all is well done.
Some information about my WorkStation:
Operating System: Ubuntu 12.04 LTS 64bit
NWChem issue: 6.1 for Debian, installed following the instruction found here from Edoapra:
http://nwchemgit.github.io/Special_AWCforum/st/id602/Running_NWChem_in_parallel.ht...
Someone knows how can I fix it?
Thank you in advance for your attention
Best Regards
Alessio
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