[gmx-users] re: .HTP FILE

Chandan Choudhury iitdckc at gmail.com
Thu Jan 10 07:16:14 CET 2013

Hi Boopathi,

Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of
gromacs manual 4.5.4. Please refer the manual.


Chandan kumar Choudhury
NCL, Pune

On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi <
boopathiphd at gmail.com> wrote:

> Dear All
>                 I  have created the pdb file for interaction of protein
> with new molecules. I am able to rum the pdb file successfully  but I am
> facing error in the Equillibration process. The Error shows that
>                                         *atom HAQ is missing in residue NIC
> 8 in the pdb file You might need to add atom HAQ to the hydrogen database
> of building block NIC  in the file aminoacids.hdb (see the manual)
> *
>                  likewise 14 atoms H atoms are missing in residu*e.Can
> anyone help me  how to add atom in .htp file for new molecules interacting
> with protein.Thanks in advance.
> with regards
> Boopathi.s
> *
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