VMD-L Mailing List

From: Manoj Dhiman (manoj1733_at_gmail.com)
Date: Fri Feb 23 2018 - 09:22:18 CST

Thanks a lot.

On Feb 23, 2018 4:39 PM, "Lutimba Stuart" <lutimba.stuart_at_scilifelab.se>
wrote:

> Hej how do you merge the two atoms, there various ways of merging specific
> atoms but the one i trust is the use of the psfgen plugin which specifys
> the topology files in respect to your atom types. Some atoms disappeared in
> your case because they were not defined when merging them. If you use
> psfgen this will solve everything, you can also decide to use pathes.
>
> On Fri, Feb 23, 2018 at 10:34 AM, Manoj Dhiman <manoj1733_at_gmail.com>
> wrote:
>
>> Dear users,
>>
>> I am trying to solvate a molecule by following axel's tutorial
>> https://sites.google.com/site/akohlmey/software/topo
>> tools/topotools-tutorial---various-tips-tricks. The strange thing is
>> that molinfo command transfers the information as it is to the top
>> molecule, without changing the atom type integer to a new value. In detail,
>> the solute molecule with atom, different from oxygen and hydrogen, has atom
>> type integer equal to 1 in its pdb and psf file and the water molecule has
>> 1 and 2 for O and H, after merging though the total number of atoms,
>> angles, bonds and dihedral are correct but atom types are only 1 and 2,
>> rather than 1 2 and 3. HELP!!!
>>
>> --
>> *Regards:*
>> *Manoj Dhiman*
>>
>
>