Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

hi justin & gmx-users, meanwhile i had understood that the reference distance in the speconds file is not an upper boundary for possible bonds but the distance itself +/-x. i should have read the manual with more attention before writing to the list. thanks again, vedat dear gmx users/te

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

never mind just found it in your input pdb sorry.  Is it at the end?   Gesendet: Samstag, 07. Juni 2014 um 16:32 Uhr Von: "Vedat Durmaz" An: "Discussion list for GROMACS users" Betreff: [gmx-users] specbond identified by pdb2gmx but not added to topology dear gmx users/team

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

: Samstag, 07. Juni 2014 um 16:32 Uhr Von: "Vedat Durmaz" An: "Discussion list for GROMACS users" Betreff: [gmx-users] specbond identified by pdb2gmx but not added to topology dear gmx users/team, i've defined some simple residues (5 monomeric units) in aminoacids.rtp, residu

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

On 6/7/14, 10:32 AM, Vedat Durmaz wrote: dear gmx users/team, i've defined some simple residues (5 monomeric units) in aminoacids.rtp, residues.dat and aminoacids.hdb that i want to use for the modelling of small polymers. the polymer may be highly bifurcated due to a branching T piece among t

[gmx-users] specbond identified by pdb2gmx but not added to topology

dear gmx users/team, i've defined some simple residues (5 monomeric units) in aminoacids.rtp, residues.dat and aminoacids.hdb that i want to use for the modelling of small polymers. the polymer may be highly bifurcated due to a branching T piece among the monomer units. all possible intermol