Missed Atoms in Fragment file

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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

  1. This is an automatically generated fragment file
  2. Atom types and connectivity were derived from coordinates
  3. Atomic partial charges are crude estimates
  4. 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://www.nwchem-sw.org/index.php/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

  • Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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You need to have a fragment file for any nonstandard residues. NWChem will try to generate rough version of it, but you need to go in and fix it, including filling in atom types. It is no different from other force field codes.

Marat


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