[gmx-users] general question about molecule.rtp and pdb2gmx

[Valentina]

Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.

I have a few atom types and a few atoms per each atom type.

So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!

*So like this:*
[ B31 ] 
  [ atoms ]
; atomname atomtype charge chargegroup
   o1  oc15  -1.00   0
   h1  hoz    0.30  0
   o2  oc18  -0.875   1
   h2  hoy    0.350  1
   o3  oc21  -0.875   1
   h3  hoy    0.350  1
   o4  oc17  -0.875   2
   h4  hoy    0.350  2
   mg1 mg    1.40    3
   al1 ac3    1.35   4
   o5  oc16  -0.875   5
   h5  hoy    0.350  5
   o6  oc20  -0.875   2
   h6  hoy    0.350  2
   o7  oc19  -0.875   5
   h7  hoy    0.350  5
   o8  oc15   -1.00    6
   h8  hoz    0.30  6
   mg2 mg   1.40   7
   mg3 mg   1.40   8
  [ bonds ]
 ; atom1 atom2   parametersindex
   oc15 hoz b_oc-h
   oc16 hoy b_oc-h
   oc17 hoy b_oc-h
   oc18 hoy b_oc-h
   oc19 hoy b_oc-h
   oc20 hoy b_oc-h
   oc21 hoy b_oc-h
  ac3 	oc16	a_oc-ac-h
  ac3 	oc17	a_oc-ac-h
  ac3 	oc18	a_oc-ac-h
  ac3 	oc19	a_oc-ac-h
  ac3 	oc20	a_oc-ac-h
  ac3 	oc21	a_oc-ac-h

*Rather than like this:*
[ B31 ] ;
  [ atoms ]
; atomname atomtype charge chargegroup
   o1  oc15  -1.00   0
   h1  hoz    0.30  0
   o2  oc18  -0.875   1
   h2  hoy    0.350  1
   o3  oc21  -0.875   1
   h3  hoy    0.350  1
   o4  oc17  -0.875   2
   h4  hoy    0.350  2
   mg1 mg    1.40    3
   al1 ac3    1.35   4
   o5  oc16  -0.875   5
   h5  hoy    0.350  5
   o6  oc20  -0.875   2
   h6  hoy    0.350  2
   o7  oc19  -0.875   5
   h7  hoy    0.350  5
   o8  oc15   -1.00    6
   h8  hoz    0.30  6
   mg2 mg   1.40   7
   mg3 mg   1.40   8
  [ bonds ]
 ; atom1 atom2   parametersindex
   o1 h1 b_oc-h
   o2 h2 b_oc-h
   o3 h3 b_oc-h
   o4 h4 b_oc-h
   o5 h5 b_oc-h
   o6 h6 b_oc-h
   o7 h7 b_oc-h
   o8 h8 b_oc-h
   al1	o5	a_oc-ac-h
   al1	o4	a_oc-ac-h
   al1	o2	a_oc-ac-h
   al1	o7	a_oc-ac-h
   al1	o6	a_oc-ac-h
   al1	o3	a_oc-ac-h


If I use the 1st I get .top that does not list interactions, just [ atoms ]
and #include link to the FF. Is this still OK? Does it read the [ bonds ]
interactions or just non bonded?

Thank you,
V





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