Hi, On Thu, Aug 6, 2015 at 9:02 AM Zhenhai Li <[email protected]> wrote:
> Hi Aishwary, > > Thank you very much for your reply. So I guess the answer to my question is > there's no way to overwrite the angle function type for specific angle > interaction by changing .rtp file or other like ffbond.itp files in force > field. Then I will save my time from investigating how to change .rtp file > or other files in force field folder, and focus on writing a script. > I would have expected [angles] N C O 5 1000.0 120.0 ; ie whatever the actual parameters are would over-ride the default (ie. angletype of 3 and let grompp look up the parameters) but I'm not sure that that's what your original post claims. Mark > Thanks a lot. > > Zhenhai > > > > Date: Thu, 6 Aug 2015 09:44:26 +0530 > > From: Aishwary Shivgan <[email protected]> > > To: [email protected] > > Subject: Re: [gmx-users] Question about generating top file with > > different angle functions. > > Message-ID: > > <CAJ= > > [email protected]> > > Content-Type: text/plain; charset=UTF-8 > > > > 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 <[email protected]> > > 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 > > > > > > -- > > > Zhenhai > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * 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 [email protected]. > > > > > > > > > -- > Zhenhai > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * 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 [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * 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 [email protected].
