[gmx-users] Structure breaking during minimization

[Apramita Chand]

Dear Justin,
My .rtp entry for taurine is
[TAU]
  [ atoms ]
      O3    OM   -0.607     1
      S1    SDmso 0.849     1
      O1    OM   -0.607     1
      O2    OM   -0.607     1
      C2    CH2  -0.039     2
      C1    CH2   0.376     2
      N1    NL   -0.469     3
      H5    H     0.368     3
      H6    H     0.368     3
      H7    H     0.368     3
   [ bonds ]
      OM    SDmso   gb_25
      SDmso CH2     gb_32
      CH2   CH2     gb_26
      NL    H       gb_2
   [ angles]
     OM   SDmso  CH2   ga_46
     SDmso CH2   CH2   ga_16
     CH2   NL    H     ga_11
     H     NL    H     ga_10

Why does it break during minimization? The .pdb file was downloaded from
ATB server and charges have been assigned from the .itp file .

What could be wrong?
If I optimize a structure using Gaussian and use that structure and charges
for running in GROMOS53a6 ff , should I make an rtp file and assign atom
types,bond types from GROMOS ff which seem to match with my actual
structure . What is the procedure here?


Regards,
Apramita