Hi Case,
I appreciate your kindly assistance by referring my problems to Junmei.
On 11/15/11, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Nov 14, 2011, Crystal.CHIA-YU Ku wrote:
>>
>> Besides, acdoctor seemed not to
>> run successfully.
>
> [I'm cc-ing this to Junmei: Junmei: please see the attached pdb file, and
> note
> the that acdoctor indeed fails. It seems to think that bondnum is zero, as
> well as numh.]
>
>
>> Now I suspect if the major problem probably is from
>> my ligand's pdb file, even if I cannot perceive problems on Chimera
>> and AutodockTool.
>
> It is indeed a very strange ligand. It looks like the charge should be -1,
> not +1. But it is not just an sqm problem: Gaussian 09 is unable to obtain
> SCF convergence on the first step, either. You might try to break the
> molecule into smaller pieces to see if that helps: the five-membered ring
> is certainly a likely suspect. Others on the list might want to look at the
> PDB file to see something.
Could you let me know how I break down the ligand structure to figure
out where the charge problem comes from?
>
> How did you obtain the pdb file? Did you manipulate it from its original
> state?
I am not sure what level of manipulation can be called manipulation,
but when I prepared pdb file of ligand, I deleted the connectivity of
the ligand to magnesium ions, and added H atom by Chimera.
Here is my way to obtain the ligand from the crystal structure of
ligand-receptor:
1. Download the ligand-receptor crystal structure file: 2HOM in PDB.
The structure file has no hydrogen inside.
2. Copy atom coordinates of the ligand and their connectivity to
another empty file, then store them as TPS.pdb.
I copied the atom coordinates from HETATM 1689 to HETATM 1710, and
copied the connectivity from CONECT 1689 to CONECT 1710. In addition,
I deleted the unnecessary connectivity of the ligand atoms to the two
magnisum ions HETATM 1683, HETATM 1684.
I just try to make the connectivity clear because my ligand pdb has no
magnisum ions inside and avoid having more complex problems after
putting charge information of the ligand and receptor together.
3. Use Chimera to add hydrogen atoms to the ligand, and then save it
as TPS_MD1.pdb which I already provided in the last email.
The only difference between original ligand information and the ligand
processed by Chimera is that the hydrogen number of ligand handled by
Chimera only provides 16 hydrogen, but the original ligand information
says the ligand has 18 hydrogens. I cannot add two hydrogens to the
phosphate group of my ligand by Chimera. Here is the information in
the crystal structure about the ligand:
FORMUL 8 TPS C12 H18 N4 O4 P S 1+
4. Run antechamber...(fail several times... when use default
setting.) But antechamber could run when I modified values of
tight_p_conv and scfconv, but results are miserable. SQM energy always
is around 103.7426 kcal/mol, and parmchk could not figure out the
missing angle, so it has not been possible to generate parameter files
of the ligand.
Here are conditions I tried and antechamber could run:
tight_p_conv=1, scfconv=1.d-7
tight_p_conv=0, scfconv=1.d-8
tight_p_conv=0, scfconv=1.d-9
tight_p_conv=0, scfconv=1.d-10
For the charge problem, I think there is a positive charge on the five
member ring. I also checked ligand information in the original crystal
structure file and it says the ligand carries one postive charge (the
information is in "FORMUL" above).
The attachment is the original file for my receptor and ligand as your
reference. I prepare ligand pdb file and receptor file both from this
file.
Sincerely,
Crystal
>
> ...dac
>
>
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Received on Tue Nov 15 2011 - 14:30:04 PST
