Re: [gmx-users] ligand-protein distance restraint

Pathumwadee Intharathep wrote: Dear Mark, I tried to make a hybrid [moleculetype] section that includes one protein and 4 ligands, it is very complicate way to do. I have to do mannaully to put [atoms], [bonds], [pairs], [angles] and [dihedral] for each ligand and need to re-number for all,

[gmx-users] ligand-protein distance restraint

Dear Mark,   I tried to make a hybrid [moleculetype] section that includes one protein and 4 ligands, it is very complicate way to do.   I have to do mannaully to put [atoms], [bonds], [pairs], [angles] and [dihedral] for each ligand and need to re-number for all, if not, the error of "Atoms in

[gmx-users] ligand-protein distance restraint

Dear gmx-user,   I put #include "disre.itp"   at the end of making a hybrid [molecule] section as mark's suggestion, I got the same error after grompp.    “Fatal error: [ file "../disre.itp", line 2 ]: Atom index (195) in distance_restraints out of bounds (1-1)”   ; 

Re: [gmx-users] ligand-protein distance restraint

Pathumwadee Intharathep wrote: Dear Mark, I put #include "disre.itp" at the end of making a hybrid [molecule] section as you've suggested, I got the same error after grompp. No, you didn't put it at the end of a [moleculetype] section. These must all start and finish before the [system]

[gmx-users] ligand-protein distance restraint

Dear Mark,   I put #include "disre.itp"   at the end of making a hybrid [molecule] section as you've suggested, I got the same error after grompp.    “Fatal error: [ file "../disre.itp", line 2 ]: Atom index (195) in distance_restraints out of bounds (1-1)”   ;   File 'top.top'

[gmx-users] ligand-protein distance restraint

Mark's suggestion of a hybrid [molecule] section is a good one. Please note the need to then include disre=simple in your .mdp file. Mark has previously posted an enhancement request for a grompp warning if you forget disre=simple in the .mdp file response to some confusion that I previousl

Re: [gmx-users] ligand-protein distance restraint

Pathumwadee Intharathep wrote: Dear gmx-users, Do you know how to make distance restraint between ligand and protein in gromacs? I have a chain of protein binds with 4 drugs in water-lipid box, the topology put below.. ; File 'top.top' was generated; Include forcefield parameters ; #i

[gmx-users] ligand-protein distance restraint

Dear gmx-users,   Do you know how to make distance restraint between ligand and protein in gromacs? I have a chain of protein binds with 4 drugs in water-lipid box, the topology put below.. ;   File 'top.top' was generated; Include forcefield parameters ; #include "/home/bio001/02_saow/grom