[gmx-developers] adding formal charges in trjconv

Berk Hess hessb at mpip-mainz.mpg.de
Wed Oct 8 10:51:51 CEST 2008


I guess the question was not phrased properly.
On the users list Omer had a question about trjconv (not) writing 
charges to pdb.
I guess this is the same question.

I just checked the pdb file format.
There is a filed of two characters for the charge of an atom.
But this would only be an integer charge, i.e. the charge of an ion.
Is this what you want, or do you want the partial charges of each atom?


David van der Spoel wrote:
> Omer Markovitch wrote:
>> Hello,
>> As I understand, in version 3.3.3 no formal charges are written.
>> I would like to suggest that in future GROMACS versions, there will 
>> be an option to print formal charges, as they appear in the topology 
>> file.
>> Thank you, Omer.
> Both gromp and pdb2gmx print the overall charge. Or do you want them 
> per residue?
>> Koby Levy research group,
>> Weizmann Institute of Science.
>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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