problem encountered when running prepare
Just Got Here
12:10:12 PM PST - Fri, Feb 18th 2011
Hi, NWChem users,
   I encountered a problem"  Unresolved atom types in fragment" when running NWChem prepare module. I think it's because the molecule I studied are not included in the amber and charmm force field. The molecule is Epoxide. I searched online, it says I should use the mm2 force field, but I cann't find this force field in the NWChem data file. Does any one have any suggestions for me to solve this problem.
--wxu Feb 18th 7:09 pm Local Time

  • Guest -
12:11:01 PM PST - Wed, Mar 2nd 2011
You need to define the appropriate atom types and charges in the fragment file, and make sure that the atom types are defined in one of the par files in your path as defined in the .nwchemrc file.

Just Got Here
3:47:52 PM PDT - Thu, Jun 9th 2011
counterion issue
Dear Dr all,

I have a problem in the system setup, namely in the "prepare" section.
The structure of my protein, in the pdb format includes some Mg atoms I would like to keep. When I load the pdb (source command) the program does not like the Mg position and then displaces them from the active site using the "add counterion module". I tried changing the grid (mgrid) and the minimum distance (rgrid) but the effects were not good. I also tried to rescale the charge of the ion (counter -0.00001) as to avoid replacement.
Is there a way to avoid altogether this automatic displacement of crystallographic ions? I just want to keep my ions in the position they are, without adding any more, as the system is already neutral.

I thank you in advance for the help and support.
My best regards.
Marco Stenta

Clicked A Few Times
5:16:53 PM PDT - Thu, Jun 9th 2011
Can you run prepare without adding counterions and see if Mg positions are shifted. If it is the case then it is probably formatting problem in your pdb file. I could take a look at it but would need your files.

Just Got Here
12:08:25 AM PDT - Fri, Jun 10th 2011
thenks for the replay
here is my input :
it seems I am not specifically asking for counterions.

the pdb is quite big, i can send it to you is you tell me how,
below i just put the Mg part, so you can see what is wrong.
thanks a lot
It would be super cool if we menage to have it working

 start topo
  1. memory heap 10 mb stack 360 mb global 120 mb
 memory total 10000 mb

 permanent_dir ./perm

 scratch_dir ./data



prepare

 source mol2.pdb

 new_top    new_seq

 new_rst
  1. grid 24 0.1
  2. counter -100.00001

  1. center
  2. orient
 solvent name WAT model spce

 boxsize

 periodic




 ignore

 write topo_ref.rst

 write topo_ref.pdb

end

 task prepare




other residues
ATOM 25403 MG2 MG2 1495 75.518 68.889 58.745 1.00 0.00
ATOM 25404 MG2 MG2 1496 73.764 83.919 63.441 1.00 0.00
ATOM 25405 MG2 MG2 1497 74.060 80.332 62.930 1.00 0.00
ATOM 25406 MG2 MG2 1498 78.202 62.968 31.553 1.00 0.00
ATOM 25407 MG2 MG2 1499 88.932 76.146 77.037 1.00 0.00
ATOM 25408 MG2 MG2 1500 102.309 89.279 63.686 1.00 0.00
ATOM 25409 MG2 MG2 1501 73.048 76.889 53.994 1.00 0.00
ATOM 25410 MG2 MG2 1502 56.241 96.811 56.351 1.00 0.00
ATOM 25411 MG2 MG2 1503 42.982 67.892 69.772 1.00 0.00
ATOM 25412 MG2 MG2 1504 42.393 84.006 66.473 1.00 0.00
ATOM 25413 MG2 MG2 1505 42.215 80.486 66.789 1.00 0.00
ATOM 25414 MG2 MG2 1506 36.941 66.226 99.451 1.00 0.00
ATOM 25415 MG2 MG2 1507 24.601 75.620 51.610 1.00 0.00
ATOM 25416 MG2 MG2 1508 14.087 95.027 68.434 1.00 0.00
ATOM 25417 MG2 MG2 1509 44.372 76.075 77.089 1.00 0.00
ATOM 25418 MG2 MG2 1510 60.481 94.094 73.850 1.00 0.00
ATOM 25419 MG2 MG2 1511 69.261 106.930 48.247 1.00 0.00
ATOM 25420 MG2 MG2 1512 50.465 96.694 81.202 1.00 0.00
ATOM 25421 MG2 MG2 1513 51.722 88.990 89.830 1.00 0.00
ATOM 25422 MG2 MG2 1514 64.150 88.025 40.255 1.00 0.00
ATOM 25423 MG2 MG2 1515 37.994 106.896 85.718 1.00 0.00
ATOM 25424 MG2 MG2 1516 65.814 95.381 47.981 1.00 0.00
ATOM 25425 MG2 MG2 1517 32.273 82.203 37.039 1.00 0.00
ATOM 25426 MG2 MG2 1518 82.927 83.179 93.041 1.00 0.00
water
the topo.seq file looks all right

Clicked A Few Times
9:27:54 AM PDT - Fri, Jun 17th 2011
The best thing is to send me tar file of your run, so I can run it on my side. My address is
marat dot valiev at pnl dot gov

Clicked A Few Times
10:10:42 AM PDT - Wed, Sep 7th 2011
I have same problem with prepare task.

input file:
echo

scratch_dir /media/science/tmp
permanent_dir /media/science/nwchem-data/
memory total 8192 mb
start diamond
title "diamond"

prepare
 system diamond_em
 new_top new_seq
 solvate
end

task prepare

md
 system diamond_em
 sd 100
end

task md optimize

I try pdb-files:
1 - http://www.wellesley.edu/Chemistry/Flick/molecules/diamond.pdb
2 - http://www.bris.ac.uk/Depts/Chemistry/MOTM/diamond/diamond.pdb
3 - and ?reated in gabedit 2.3.7 3x3x3 unit cell

Just Got Here
9:53:59 AM PDT - Fri, Oct 12th 2012
Quote:Marat Jun 9th 5:16 pm
Can you run prepare without adding counterions and see if Mg positions are shifted. If it is the case then it is probably formatting problem in your pdb file. I could take a look at it but would need your files.


Dear Marat,
I have the same problem as well: I need the MG2 ion at the binding site as it is in my original pdb file but the prepare command changes its location. Would you please let me know how I can fix it.

Best,
Hassan.

Clicked A Few Times
8:29:43 PM PDT - Thu, Oct 18th 2012
Check if Mg atom name starts at column 13.


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