[gmx-users] Format of a Topology File When Using Amber FF in Gromacs

[한상화]

Dear Gromacs users,

 

I have successfully installed Amber FF in Gromacs according to the
instruction by the Pande Group (http://folding.stanford.edu/ffamber/).

I ran a demo successfully and enjoyed the speed of Gromacs.

My questions are:

[Question 1] The topology file produced by pdb2gmx with Amber FF
(ffamber03, for example) looked different from what we used to obtain with
ffG43a1.

No force constants were assigned in [ bonds ], [ angles ], [ dihedrals ],
etc.

 

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
chargeB      massB
     1 amber99_25      1    DA5    H5T      1     0.4422      1.008   ;
qtot 0.4422
     2 amber99_43      1    DA5    O5'      2    -0.6318         16   ;
qtot -0.1896
     3 amber99_11      1    DA5    C5'      3    -0.0069      12.01   ;
qtot -0.1965
.......

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    2     3     1 
    3     4     1 
.......

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     4     1 
    1     5     1 
    1     6     1 
.......

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
c3
    1     2     3     1 
    2     3     4     1 
    2     3     5     1 
.....

 

[Question 2] In the RTP file of Amber FF, again no force constants were
assigned in [ bonds ], [ dihedrals ], etc., and [ angles ] was missing.

Is it what it’s supposed to be?

Here is a sample rtp entry of ffamber03.rtp.

 

[ GLY ] ; HAx atoms assigned new ff03 atom type
 [ atoms ]
     N    amber99_34  -0.374282    1
     H    amber99_17   0.253981    2
    CA    amber99_11  -0.128844    3
   HA1    amber99_0    0.088859    4
   HA2    amber99_0    0.088859    5
     C    amber99_2    0.580584    6
     O    amber99_41  -0.509157    7
 [ bonds ]
     N     H
     N    CA
    CA   HA1
    CA   HA2
    CA     C
     C     O
    -C     N
 [ dihedrals ]
    CA     C    +N    +H    backbone_prop_1
     O     C    +N    +H    backbone_prop_2
    -C     N    CA    CB    backbone_prop_3
    -C     N    CA     C    backbone_prop_4
    CA     C    +N   +CA    backbone_prop_1
     O     C    +N   +CA    backbone_prop_1
    -C     N    CA   HA1    backbone_prop_5
    -C     N    CA   HA2    backbone_prop_5
   HA1    CA     C    +N    backbone_prop_6
   HA2    CA     C    +N    backbone_prop_6
 [ impropers ]
    -C    CA     N     H
    CA    +N     C     O
                        
Any comments would be appreciated.

 

Sanghwa Han

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