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

[David van der Spoel]

한상화 wrote:
> 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.
all this information is derived from the atomtypes and can be found in
ffamberxxxbon.itp

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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