[gmx-users] (no subject)

http://tgiturkiye.net/breakingnews/63LeePhillips/";>http://tgiturkiye.net/breakingnews/63LeePhillips/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before post

[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)”   ; 

[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

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

[gmx-users] distance restrain

Dear gmx-users,   How can I make the distance restrain between molecules such as protein and ligand?   thanks in advance   pathum   ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please searc

[gmx-users] position and distance restrain

Dear  gmx-user,   Do I define position and distance restrain simulteneusly? my md.mdp has set as below but it works only for position restrain.   title   = M2_amand in POPC cpp =  /lib/cpp define  =  -DPOSRES define  =  -DDISRES constraints  

[gmx-users] flood of gmx's mails in my mailbox

Dear gmx-user,   My mailbox has flood of gmx's mails. What should I do to digest them.   Best regards,   pathumwadee  ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] distance restraint

Dear gmx's user, May I asked you some technicl Questions? Do you know how to make distance restraint in gromacs? what I did I have created file name "disre.itp" as shown below [ distance_restraints ] ;   ai    aj type index type low up1 up2 fac    489   1133   1   1 1   0.25 0.35 0.40 1.0