On Sun, Jan 10, 2021, Eduardo R. Almeida wrote:
>
>I am sending you a link of this PDB file:
>
The problem is in chain H:
==========================================================================
ATOM 96642 O WAT H 1 48.978 69.478 169.716 1.00 0.00 O
ATOM 96643 H1 WAT H 1 49.003 70.081 170.459 1.00 0.00 H
ATOM 96644 H2 WAT H 1 48.150 69.672 169.277 1.00 0.00 H
TER 96645 WAT H 1
ATOM 96645 O WAT H 1 61.857 14.621 145.663 1.00 0.00 O
ATOM 96646 H1 WAT H 1 61.286 13.860 145.771 1.00 0.00 H
ATOM 96647 H2 WAT H 1 62.733 14.250 145.555 1.00 0.00 H
TER 96648 WAT H 1
ATOM 96648 O WAT H 1 57.472 23.159 177.642 1.00 0.00 O
ATOM 96649 H1 WAT H 1 58.357 23.279 177.986 1.00 0.00 H
ATOM 96650 H2 WAT H 1 57.596 23.029 176.702 1.00 0.00 H
TER 96651 WAT H 1
ATOM 96651 O WAT H 1 11.708 50.131 248.596 1.00 0.00 O
ATOM 96652 H1 WAT H 1 10.999 50.507 248.075 1.00 0.00 H
ATOM 96653 H2 WAT H 1 11.263 49.631 249.281 1.00 0.00 H
TER 96654 WAT H 1
ATOM 96654 O WAT H 1 11.888 60.095 235.789 1.00 0.00 O
ATOM 96655 H1 WAT H 1 11.755 60.015 236.734 1.00 0.00 H
ATOM 96656 H2 WAT H 1 12.838 60.046 235.677 1.00 0.00 H
TER 96657 WAT H 1
ATOM 96657 O WAT H 1 40.670 8.101 163.317 1.00 0.00 O
ATOM 96658 H1 WAT H 1 40.617 7.212 163.668 1.00 0.00 H
ATOM 96659 H2 WAT H 1 41.348 8.525 163.841 1.00 0.00 H
TER 96660 WAT H 1
ATOM 96660 O WAT H 1 0.908 55.775 147.759 1.00 0.00 O
ATOM 96661 H1 WAT H 1 0.855 54.880 148.094 1.00 0.00 H
ATOM 96662 H2 WAT H 1 1.584 55.738 147.082 1.00 0.00 H
TER 96663 WAT H 1
ATOM 96663 O WAT H 1 53.740 29.555 207.584 1.00 0.00 O
ATOM 96664 H1 WAT H 1 54.452 29.069 207.168 1.00 0.00 H
ATOM 96665 H2 WAT H 1 53.619 30.326 207.029 1.00 0.00 H
TER 96666 WAT H 1
ATOM 96666 O WAT H 1 14.060 40.377 230.866 1.00 0.00 O
ATOM 96667 H1 WAT H 1 14.848 40.794 230.517 1.00 0.00 H
ATOM 96668 H2 WAT H 1 13.895 40.831 231.693 1.00 0.00 H
TER 96669 WAT H 1
ATOM 96669 O WAT H 1 35.779 13.583 185.513 1.00 0.00 O
ATOM 96670 H1 WAT H 1 35.872 12.931 184.819 1.00 0.00 H
ATOM 96671 H2 WAT H 1 36.583 14.100 185.466 1.00 0.00 H
TER 96672 WAT H 1
ATOM 96672 O WAT H 2 63.561 22.593 152.813 1.00 0.00 O
ATOM 96673 H1 WAT H 2 62.613 22.558 152.945 1.00 0.00 H
ATOM 96674 H2 WAT H 2 63.805 23.485 153.060 1.00 0.00 H
==========================================================================
There are ten waters all with residue number 1, same for residue numbers
2 through 84. Then the pattern changes, and each new water molecule again gets
a new residue number.
I don't know why packmol did this, and only for part of one chain. This is
technically illegal, since you have ten waters with the same chainId and the
same residue number. (I'm blaming this on packmol, but is it possible that
the origin of this odd behavior is somewhere else?)
But it's also true that tleap is not doing what I thought it would do: it
apparently only increases its internal residue number when it sees an input
residue number that is different from the previous one. But a "TER" card
should also be triggering an increment to the internal residue number.
I'm cc-ing this to our tleap expert, Scott Brozell. Scott, (or anyone else
who wants to help!) see the "wat.pdb" file attached. If you apply these
tleap commands:
source leaprc.water.spce
x = loadPdb wat.pdb
you will see duplicate atoms message that should not be there. Not sure how
easy/hard it would be to change this: might be as simple as setting the
current residue number to -99999 when a TER card is encountered: then the
next residue number (whatever it is) will be different from the previous
one.
Eduardo: I've attached a simple script to update the residue numbers in
chain H is attached. Run this as fix_chainH < com_mem.pdb > new_name.pdb.
...good luck....dac
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Received on Sun Jan 10 2021 - 08:00:02 PST
