Dear all,
Futher to my last email I would like to give more detail about my mutant.pdb
file.
David Case wrote:
> You should(?) be able to figure out what is going on by looking at the pdb
> file. For some reason, LEaP thinks there are 10 H1 atoms in a single residue.
> Make sure that the residue numbers are unique. Since you have more than
> 10000 residues, this may be a problem with residue numbering: check that
> you don't have "*****" or somehting like that as a residue number in the
> pdb file.
I don't have any ***** in the mutant.pdb file created by Xleap but MG and Na+
ions are now at the end of pdb file instead of water molecules and some water
molecules get deleted. The mutant.pdb file looks like this:
.
.
.
TER 58754 WAT 11780
ATOM 58755 H1 WAT 11781 -27.405 -11.267 1.246 1.00 0.00
ATOM 58756 H2 WAT 11781 -28.687 -12.065 1.345 1.00 0.00
ATOM 58757 O WAT 11781 -28.109 -11.495 1.852 1.00 0.00
TER 58758 WAT 11781
ATOM 58759 H1 WAT 11782 -40.978 40.873 8.086 1.00 0.00
ATOM 58760 H2 WAT 11782 -39.662 40.129 8.164 1.00 0.00
ATOM 58761 O WAT 11782 -40.320 40.440 7.542 1.00 0.00
TER 58762 WAT 11782
ATOM 58763 H1 WAT 11783 24.813 22.181 52.708 1.00 0.00
ATOM 58764 H2 WAT 11783 25.669 22.382 53.940 1.00 0.00
ATOM 58765 O WAT 11783 25.106 21.741 53.506 1.00 0.00
TER 58766 WAT 11783
ATOM 58767 MG MG 975 48.547 67.828 63.471 1.00 0.00
TER 58768 MG 975
ATOM 58769 MG MG 976 46.479 68.205 58.972 1.00 0.00
TER 58770 MG 976
ATOM 58771 MG MG 977 52.947 69.861 58.634 1.00 0.00
TER 58772 MG 977
ATOM 58773 MG MG 978 76.526 52.517 27.746 1.00 0.00
TER 58774 MG 978
ATOM 58775 MG MG 979 76.285 50.564 32.569 1.00 0.00
TER 58776 MG 979
ATOM 58777 MG MG 980 75.745 56.664 31.946 1.00 0.00
TER 58778 MG 980
ATOM 58779 Na+ Na+ 981 92.877 49.241 57.223 1.00 0.00
TER 58780 Na+ 981
ATOM 58781 Na+ Na+ 982 113.057 34.282 19.390 1.00 0.00
TER 58782 Na+ 982
ATOM 58783 Na+ Na+ 983 27.938 51.635 51.666 1.00 0.00
TER 58784 Na+ 983
ATOM 58785 Na+ Na+ 984 44.356 29.245 36.992 1.00 0.00
TER 58786 Na+ 984
ATOM 58787 Na+ Na+ 985 80.728 56.971 29.767 1.00 0.00
TER 58788 Na+ 985
ATOM 58789 Na+ Na+ 986 26.499 87.735 72.051 1.00 0.00
TER 58790 Na+ 986
ATOM 58791 Na+ Na+ 987 45.796 35.909 49.056 1.00 0.00
TER 58792 Na+ 987
ATOM 58793 Na+ Na+ 988 27.320 79.029 45.832 1.00 0.00
TER 58794 Na+ 988
.
.
.
END
Whereas the native.pdb file which is what the mutant.pdb file should look like
is:
.
.
.
ATOM 15655 O LYL 974 73.716 50.840 39.316
ATOM 15656 OXT LYL 974 73.652 49.131 37.874
TER
ATOM 15657 MG MG 975 48.547 67.828 63.471
TER
ATOM 15658 MG MG 976 46.479 68.205 58.972
TER
ATOM 15659 MG MG 977 52.947 69.861 58.634
TER
ATOM 15660 MG MG 978 76.526 52.517 27.746
TER
ATOM 15661 MG MG 979 76.285 50.564 32.569
TER
ATOM 15662 MG MG 980 75.745 56.664 31.946
TER
ATOM 15663 Na+ Na+ 981 92.877 49.241 57.223
TER
ATOM 15664 Na+ Na+ 982 113.057 34.282 19.390
TER
.
.
.
TER
ATOM 15686 Na+ Na+ 1004 56.742 78.687 35.164
TER
ATOM 15687 Na+ Na+ 1005 66.970 28.464 42.514
TER
ATOM 15688 Na+ Na+ 1006 103.515 47.708 77.512
TER
ATOM 15689 Na+ Na+ 1007 89.346 75.677 -0.071
TER
ATOM 15690 Na+ Na+ 1008 84.219 35.572 23.776
TER
ATOM 15691 O WAT 1009 79.142 30.193 42.275
ATOM 15692 H1 WAT 1009 79.469 30.540 41.445
ATOM 15693 H2 WAT 1009 79.930 29.948 42.759
TER
ATOM 15694 O WAT 1010 72.984 91.438 12.587
ATOM 15695 H1 WAT 1010 73.501 90.721 12.220
ATOM 15696 H2 WAT 1010 72.271 91.004 13.056
TER
.
.
TER
ATOM 96169 O WAT 27835 26.110 92.172 21.672
ATOM 96170 H1 WAT 27835 26.552 92.914 22.085
ATOM 96171 H2 WAT 27835 26.807 91.703 21.214
TER
ATOM 96172 O WAT 27836 -27.155 -5.078 -3.695
ATOM 96173 H1 WAT 27836 -27.997 -4.642 -3.827
ATOM 96174 H2 WAT 27836 -27.043 -5.624 -4.473
TER
ATOM 96175 O WAT 27837 -19.640 22.305 53.995
ATOM 96176 H1 WAT 27837 -19.264 21.622 54.551
ATOM 96177 H2 WAT 27837 -19.902 21.847 53.196
TER
ATOM 96178 O WAT 27838 25.106 21.741 53.506
ATOM 96179 H1 WAT 27838 24.813 22.181 52.708
ATOM 96180 H2 WAT 27838 25.669 22.382 53.940
TER
END
Please, if anyone has any suggestions or advice of what I should do to get the
correct pdb file with correct number of water molecules and solvent box, could
you please let me know.
Thank you very much again.
Sally
--
-------------------------------------------------------------------------------
Salinthip Thipayang (Miss)
PhD Research Student
Biological and Biophysical Chemistry Research Group
Chemistry Department
Imperial College of Science, Technology and Medicine
Exhibition Road
London SW7 2AY
The United Kingdom
Tel: +44(0)207 5945851
Fax: +44(0)207 5945845
Email: salinthip.thipayang_at_ic.ac.uk
--------------------------------------------------------------------------------
Received on Tue Jul 23 2002 - 08:21:23 PDT
