I want to study the H-bonding interaction of two molecules. The following is
what i did:
1. download 3D molecule of estradiol and methacrylic acid from SciFinder, save
it as pdb files.
2. With Amber 8, use antechamber, parmchk, and xleap to modify the pdb file,
save.
3. Open the modified pdb files in ViewLite and bring them to proximity for
H-bond interaction, save the file as "complex.pdb",the two molecules were
named as "BE2" and "MAA". here is the file looks like:
ATOM 1 C7 BE2 1 0.035 1.199 -0.000 1.00 0.00
ATOM 2 C10 BE2 1 0.872 2.543 -0.032 1.00 0.00
....
ATOM 44 H86 BE2 1 -6.124 -2.328 -0.042 1.00 0.00
TER
ENDMDL
TER
ATOM 1 C3 MAA 2 3.776 7.634 0.370 1.00 0.00
ATOM 2 H12 MAA 2 4.741 7.876 0.262 1.00 0.00
....
ATOM 12 O5 MAA 2 1.280 6.280 0.431 1.00 0.00
TER
ENDMDL
4.When i try to load it into xleap, the following messages come out:
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named C1 from MAA did not match !
!
!ABORTING.
I wonder how to make this pdb file recognized by xleap. I can load the pdb
file of single molecule but not the complex. thanks!
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Received on Sat May 28 2005 - 22:53:01 PDT
