[gmx-users] Question about generating top file with different angle functions.
aishwaryshivgan55 at gmail.com
Thu Aug 6 06:14:29 CEST 2015
Once you define the [ bondedtypes ] in the rtp file like this.
1 1 3 1 1 3 1 0
here the dihedral type function is 3 that means all the dihedrals you
define in the aminoacids.rtp file will be taken as type 3. Even I had the
the same problem, I was using function type 3 and 5, pdb2gmx takes
function 5 as 3. Not a problem you can write a script or do it manually to
replace the number 5 to 3.
On Thu, Aug 6, 2015 at 8:26 AM, Zhenhai Li <shibalagu.thu at gmail.com> wrote:
> Dear GMX-users,
> Recently I am trying to adding a residue to a force field. I have followed
> the instruction of "how to adding residue" on the website. And right now I
> can generate the top file from PDB file with pdb2gmx command. However some
> of the angle function in the residue is different from the default one in
> rtp file in the force field. Therefore there are some mistake on the angle
> function of the new residue in the top file generated by pdb2gmx. And when
> I use grompp command to generate .tpr file, I will get error like "No
> default U-B types"
> I am not sure if there's a way to define angle type for specific angle
> interaction in force field to make pdb2gmx overwrite angle function type
> for those angle interaction, or I have to manually change those angle type?
> Thank you very much
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users