ADL: mol2cnv error message: REMARK *** ERROR 1 *** Non-integral total charge..

Hong Liang hongliang.dal at gmail.com
Wed Feb 23 15:11:11 PST 2005


Dear Autodock users,

I got error message after I run "mol2cnv acceptor.mol2"

********************
REMARK *** ERROR 1 ***  Non-integral total charge (1.346) for residue AMN-   6!
REMARK *** ERROR 1 ***  Non-integral total charge (0.272) for residue SER-   7!
REMARK *** ERROR 1 ***  Non-integral total charge (0.272) for residue ALA-   8!
REMARK *** ERROR 1 ***  Non-integral total charge (0.496) for residue ILE- 276!
REMARK *** ERROR 1 ***  Non-integral total charge (0.496) for residue VAL- 340!
REMARK *** ERROR 1 ***  Non-integral total charge (-2.026) for residue ASP- 405!
REMARK *** ERROR 1 ***  Non-integral total charge (-0.026) for residue ASN- 410!
REMARK *** ERROR 2 ***  Non-integral total charge (-1.936) for residue CXL- 411!
REMARK *** ERROR 3 ***  Non-integral total charge (-1.136) for whole system!
*********************

I used Deepview to open the pdb file which was download from web. 
Deepview did some modifications (remove waters, fix missing atoms and
reconstruct sidechains). Then I use "getready" to seperate ligand and
protein.  Preparation protein in Sybyl gave the acceptor.mol2 file. 
After I run "mol2cnv" to convert mol2 to pdbq, error messages were
obtained in the .err file as above.

I saw similar questions in the list and I can not find the solution. 
How can I fix the problem?

Autodock online document addressed the problem either, saddly, it did
not tell how to solve the problem.
(http://www.scripps.edu/mb/olson/doc/autodock/getting_started/index.html).

Thanks,

Hong



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