Hi Case,
On Thu, Nov 17, 2011 at 8:33 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> Message from Junmei Wang below clears up two problems in this thread:
>
> 1. The reason acdoctor failed was because the input pdb was not formatted
> correctly. (Perhaps acdoctor should have diagnosed this problem as well,
> but once things get in the wrong columns in PDB files, it is very difficult
> to un-do the damage.)
>
I checked and compared my ligand's pdb file, the original pdb file, and the
pdb file you provided to Junmei. I could not see any column shift. I did
not know why it happened when using acdoctor...
> 2. Here is another case where mopac converges, whereas sqm and Gaussian 09
> did not. Afficianadoes of sqm convergence problems may want to see if they
> can figure out why.
>
It seems like mopac could be another way to calculate charge of my ligand.
I looked your and Jumei's code about net charge. It raised a question for
me. That is, should I believe the ligand charge information of the original
pd file from PDB or from the literature, or believe the charge calculated
based on the structure after Chimera process?
I already did the literature, even if PubChem, checked FORMUL of the
original pdb file, they all pointed out my ligand, thiamine monophosphate,
carries one positive charge. But Junmei's and your point of view is that
this ligand should carry one negative charge because two oxygen atoms of
phosphate have no hydrogen. I am getting unclear and confused with the
judgement criteria of ligand charge before running antechamber...
Sincerely,
Crystal
>
> Thanks to Junmei for the help.....dac
>
> ----- Forwarded message from Junmei Wang <junmwang.yahoo.com> -----
>
> Date: Thu, 17 Nov 2011 07:46:22 -0800 (PST)
> From: Junmei Wang <junmwang.yahoo.com>
>
> I found the lines from "ATOMÂ Â Â 10" to "ATOMÂ Â 38" shift one
> column. This is probably the reason leads to acdoctor fail. pdb format is
> very tricky and the fields must be reside in certain columns.
>
> >From the graphics, I can see the net charge of this molecule is -1.
>
> I ran the following command to assign am1bcc charges:
>
> antechamber -fi pdb -fo mol2 -i tps.pdb -o tps_am1bcc.mol2 -nc -1 -c bcc
>
> This command failed since sqm cannot converge.
>
>
> Then I replace sqm with mopac and the command can be run smoothly:
>
> antechamber -fi pdb -fo mol2 -i
> tps.pdb -o tps_am1bcc.mol2 -nc -1 -c bcc -df 0
>
> Please find the attached tps_am1bcc.mol2 file
>
> Junmei
> ----- End forwarded message -----
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 17 2011 - 17:00:02 PST
