Re: [gmx-users] Specbond.dat file

Hi, This is all specified in the .rtp file, e.g. with the plus and minus symbols on atoms in the bonds section. Look there and compare with functioning residues. Mark On Tue, May 22, 2018, 12:02 Hemalatha Jayabal wrote: > Hi, > > Thank you. > > When I used pdb2gmx

Re: [gmx-users] Specbond.dat file

Hi, Thank you. When I used pdb2gmx to generate the topology using CHARMM, I could see from the bonds section that the bonds were not created between the newly added residue i.e hydroxyproline and the following residue(glycine). But, I also noted that bonds were created between the newly added

Re: [gmx-users] Specbond.dat file

Hej, the specbond.dat file is for extra bonds between non-neighbouring residues (e.g. disulphide bridges). So if you don't need to add anything extra for your residue there if it doesn't do anything like a disulphide would. Cheers Paul On 2018-05-22 09:24, Hemalatha Jayabal wrote: Hi

[gmx-users] Specbond.dat file

Hi all, I have added a residue (Hydroxyproline) to my .rtp files and have updated the hdb and ffbonded files. While browsing through the manual about specbond.dat, it says that any "special bonds" are to be listed specifically here. Does this mean for the newly added residue also, the bond