[gmx-users] Adding TPO and SEP to G53a6 Forcefield

[lalithkumar]

Dear Dr. Justin,

Thank you for pointing out the details of error. I have missed out the
version of GROMACS I have been using and so I would like to let you know
that my version is 4.5.7. In this version ffnonbonded.itp file of the
gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interactions. I
should agree that I dont know how they can be generated and to specify
manually. So, in a crude way I can say that I have copied all the LJ 14
types from the ffG43a1p forcefield at the gromacs contributors link:
http://www.gromacs.org/Downloads/User_contributions/Force_fields

This includes the following addition lines:

; begin insert from pamac_hsnnb.itp
; [ pairtypes ]
; for LJ 14 - use same for OP as for OA 
      OP        O  1  0.0022619536  9.687375e-07
      OP       OM  1  0.0022619536  9.687375e-07
      OP       OP  1  0.0022619536  1.265625e-06
      OW       OP  1  0.0024331696   1.737e-06
       N       OP  1  0.0023475616  1.463625e-06
      NT       OP  1  0.0023475616  1.463625e-06
      NL       OP  1  0.0023475616  1.463625e-06
      NR       OP  1  0.0023475616  1.463625e-06
      NZ       OP  1  0.0023475616  1.463625e-06
      NE       OP  1  0.0023475616  1.463625e-06
       C       OP  1  0.0023009528  2.066625e-06
     CH1       OP  1  0.0025663376  2.174625e-06
     CH2       OP  1  0.0032687988  3.000375e-06
     CH3       OP  1  0.0039370168  3.907125e-06
     CH4       OP  1  0.005459888  6.59475e-06
     CR1       OP  1  0.003536086  3.24675e-06
      HC       OP  1  0.000437552  1.38375e-07
       H       OP  1           0           0
     DUM       OP  1           0           0
       S       OP  1  0.0047521952   4.068e-06
    CU1+       OP  1  0.000972602  8.053875e-08
    CU2+       OP  1  0.000972602  8.053875e-08
      FE       OP  1           0           0
    ZN2+       OP  1  0.000972602  1.09305e-07
    MG2+       OP  1  0.0003842848  6.56775e-08
    CA2+       OP  1  0.001507652  7.939125e-07
       P       OP  1  0.005773784  5.299875e-06
      AR       OP  1  0.003764374  3.53025e-06
       F       OP  1  0.0016322592  9.81225e-07
      CL       OP  1  0.0044525672  4.399875e-06
      BR       OP  1  0.0016332104  9.1035e-06
    CMET       OP  1  0.0044806276  5.1373125e-06
    OMET       OP  1  0.0022619536  1.265625e-06
     NA+       OP  1  0.00040373684  1.63125e-07
     CL-       OP  1   0.0055883  1.16325e-05
    CCHL       OP  1  0.0024394475   2.268e-06
   CLCHL       OP  1  0.004334666  4.1738625e-06
    HCHL       OP  1  0.0002920184  7.377075e-08
   SDMSO       OP  1  0.0048877412  5.216175e-06
   CDMSO       OP  1  0.0045248108  5.2475625e-06
   ODMSO       OP  1  0.0022663291  9.752175e-07
    CCL4       OP  1  0.0024394475  3.1014e-06
   CLCL4       OP  1  0.0041472796  4.01985e-06
      SI       OP  1           0           0
; end insert from pamac_hsnnb.itp

And I had copied them as is to my ffnonbonded.itp file in modified
gromos53a6.ff folder. Also, I have also modified atomtypes as per latest
versions (for example CMET to CMet).

Finally, I could pass the grompp set now and can run mdrun too successfully.
Now I need your valuable review to know whether I had done is correct or can
I do better than this way. If so please suggest some helping material
regarding process of setting user defined LJ 14 pair types interactions to
gromos53a6ff or any forcefield. And also, briefly comment on how difference
with my results by doing in the method mentioned by me and with any other
suggested method from your side.

Please let me know if any further information to be provided from my side

Thank you 

With kind regards,
Lalith

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