Dear Amber users,
I have a system with 190868 atoms, where the majority of them are related with water molecules. When I loaded this pdb file in xleap, I got the following warning:
*********************************************************
...
-- residue 19883: duplicate [ O] atoms (total 10)
-- residue 19884: duplicate [ H1] atoms (total 10)
-- residue 19884: duplicate [ H2] atoms (total 10)
-- residue 19884: duplicate [ O] atoms (total 10)
-- residue 19885: duplicate [ H1] atoms (total 10)
-- residue 19885: duplicate [ H2] atoms (total 10)
-- residue 19885: duplicate [ O] atoms (total 10)
-- residue 19886: duplicate [ H1] atoms (total 10)
-- residue 19886: duplicate [ H2] atoms (total 10)
-- residue 19886: duplicate [ O] atoms (total 10)
-- residue 19887: duplicate [ H1] atoms (total 10)
-- residue 19887: duplicate [ H2] atoms (total 10)
-- residue 19887: duplicate [ O] atoms (total 10)
-- residue 19888: duplicate [ H1] atoms (total 10)
-- residue 19888: duplicate [ H2] atoms (total 10)
-- residue 19888: duplicate [ O] atoms (total 10)
-- residue 19889: duplicate [ H1] atoms (total 10)
-- residue 19889: duplicate [ H2] atoms (total 10)
-- residue 19889: duplicate [ O] atoms (total 10)
-- residue 19890: duplicate [ H1] atoms (total 10)
-- residue 19890: duplicate [ H2] atoms (total 10)
-- residue 19890: duplicate [ O] atoms (total 10)
-- residue 19891: duplicate [ H1] atoms (total 10)
-- residue 19891: duplicate [ H2] atoms (total 10)
-- residue 19891: duplicate [ O] atoms (total 10)
-- residue 19892: duplicate [ H1] atoms (total 10)
-- residue 19892: duplicate [ H2] atoms (total 10)
-- residue 19892: duplicate [ O] atoms (total 10)
-- residue 19893: duplicate [ H1] atoms (total 10)
-- residue 19893: duplicate [ H2] atoms (total 10)
-- residue 19893: duplicate [ O] atoms (total 10)
-- residue 19894: duplicate [ H1] atoms (total 10)
-- residue 19894: duplicate [ H2] atoms (total 10)
-- residue 19894: duplicate [ O] atoms (total 10)
-- residue 19895: duplicate [ H1] atoms (total 10)
-- residue 19895: duplicate [ H2] atoms (total 10)
-- residue 19895: duplicate [ O] atoms (total 10)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
...
***************************************************************
In order to avoid this warning, I tried to modify the chain name of the water molecules. For example:
******************************
...
ATOM 86601 O WAT J9998 61.617 8.400 386.143 1.00 0.00 O
ATOM 86602 H1 WAT J9998 62.461 8.804 386.345 1.00 0.00 H
ATOM 86603 H2 WAT J9998 61.347 7.985 386.962 1.00 0.00 H
TER
ATOM 86604 O WAT J9999 19.017 25.592 8.623 1.00 0.00 O
ATOM 86605 H1 WAT J9999 18.647 26.446 8.399 1.00 0.00 H
ATOM 86606 H2 WAT J9999 18.910 25.069 7.829 1.00 0.00 H
TER
ATOM 86607 O WAT L 1 64.447 1.280 394.269 1.00 0.00 O
ATOM 86608 H1 WAT L 1 65.379 1.270 394.052 1.00 0.00 H
ATOM 86609 H2 WAT L 1 64.395 1.786 395.080 1.00 0.00 H
TER
ATOM 86610 O WAT L 2 57.123 44.348 14.437 1.00 0.00 O
ATOM 86611 H1 WAT L 2 56.874 44.151 13.534 1.00 0.00 H
ATOM 86612 H2 WAT L 2 56.291 44.413 14.906 1.00 0.00 H
TER
...
*****************************
However, It seems the xleap did not recognize these different chain names. Thus, I got the same warning aforementioned.
Besides, the big problem is: when I generate the prmtop and inpcrd files, I realize that my system contains only 188640 atoms, instead of the 190868 atoms (real number).
Could anyone help me with this problem?
Sincerely,
Eduardo.
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Received on Fri Jan 08 2021 - 16:00:02 PST
