[gmx-users] DMF topology

[Justin A. Lemkul]

Abhishek Banerjee wrote:
> Hi,
>           After long try and error and with some reference I made a 
> topology  of DMF with six site interaction using OPLS/AA and topolgen. 
> Can some tell me is it the correct format of a topology file or do i 
> need to consider any other fact.
> 

Well, having written the script, I can tell you that the format is correct.  As 
for the validity of its contents, that is up to you based on whatever model 
you're trying to use.

I would say, however, that there is one very obvious error: your molecule has a 
net charge of 0.020.

-Justin

> ;
> ;     OPLS-AA topology, built by TopolGen version 1.0 (3/21/2009)
> ;     Script written by: Justin Lemkul (jalemkul at vt.edu)
> ;     This is your molecule's topology
> ;     Check it carefully for any errors. It is not necessarily perfect!
> ;
> ;     Topology written on Sun Sep  6 15:41:15 IST 2009
> ;
> ; Include force field
> #include "ffoplsaa.itp"
> [ atomtypes ]
> C3         15.03500     0.285       A    3.80000e-01  7.11280e-01
> N          14.00670    -0.570       A    3.25000e-01  7.11280e-01
> C          12.01100     0.500       A    3.80000e-01  4.81160e-01
> H           1.00800     0.020       A    2.50000e-01  1.25520e-01
> O          15.99940    -0.500       A    2.96000e-01  8.78640e-01
> 
> [ moleculetype ]
> ; Name            nrexcl
> DMF                 3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1  C3      1    DMF     CM1      1       0.285   
> 12.01100                            
>      2   N      1    DMF     NM      1      -0.570   
> 14.00670                            
>      3  C3      1    DMF     CM2      1       0.285   
> 12.01100                            
>      4   C      1    DMF     CF     1        0.500   
> 12.01100                            
>      5   H      1    DMF     HF      1       0.020    
> 1.00800                            
>      6   O      1    DMF     OF      1      -0.500   
> 15.99940                            
> 
> [ bonds ]
> ;  ai    aj funct
>     1     2     1    0.14490        282001.6
>     2     3     1    0.14490        282001.6
>     2     4     1    0.13350       410032.0
>     4     5     1    0.10900       284512.0
>     4     6     1    0.12290       476976.0
> 
> [ pairs ]
> ;  ai    aj funct
>     1     5     1
>     1     6     1
>     3     5     1
>     3     6     1
> 
> [ angles ]
> ;  ai    aj    ak funct
>     1     2     3     1        116.200    711.280
>     1     2     4     1        121.900    418.400
>     3     2     4     1        121.900    418.400
>     2     4     5     1        109.500    292.880
>     2     4     6     1        122.900    669.440
>     5     4     6     1        123.000    292.880
> 
> [ dihedrals ]
> ;  ai    aj    ak    al funct
>     1     2     4     5     3    -0.29079  -0.87237   0.00000   
> 1.16315   0.00000   0.00000
>     1     2     4     6     3    25.47638   0.00000 -25.47638   
> 0.00000   0.00000   0.00000
>     3     2     4     5     3    -0.29079  -0.87237   0.00000   
> 1.16315   0.00000   0.00000
>     3     2     4     6     3    25.47638   0.00000 -25.47638   
> 0.00000   0.00000   0.00000
> 
> [ dihedrals ]
> ;  aj    ak    ai    al funct
>     1     3     2     4     1    improper_Z_N_X_Y
>     2     6     4     5     1    improper_O_C_X_Y
> 
> [ system ]
> ; Name
> DMF, generated by TopolGen
> 
> [ molecules ]
> ; Compound        #mols
> DMF                 1
> 
> Thanks
> abhishek
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================