Dear Gromacs users,<br> <br> <div id=":84"><div style="text-align:left">
i am adding new residue to the existing charmm27 force field of the
gromacs and i am planning to use buckingham potential for the non
bonded interactions. for that i made following changes to the
ffnonbonded.itp file<br></div>
<br> [ atomtypes ]<br>;name at.num mass charge ptype sigma epsilon<br>CC32A 6 12.01100 0.1030 A 0.0 0.0 0.0<br>HCA2 1 1.00800 0.0355 A 0.0 0.0 0.0<br>
OC30A 8 15.999400 -0.3480 A 0.0 0.0 0.0<br> [ pairtypes ]<br>; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS<br>OC30A OC30A 1 0.0 0.0<br>
OC30A CC32A 1 0.0 0.0<br>OC30A HCA2 1 0.0 0.0<br>CC32A CC32A 1 0.0 0.0<br>CC32A HCA2 1 0.0 0.0<br>HCA2 HCA2 1 0.0 0.0<br>;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)<br>
[ nonbond_params ]<br>; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS<br>OC30A OC30A 2 243922.5976 40.2414486921 0.000803746<br>OC30A CC32A 2 179625.8144 36.297640653 0.001476115 <br>
OC30A HCA2 2 85489.9984 40.899795501 0.000413379<br>CC32A CC32A 2 132277.5784 33.05785124 0.002710395<br>CC32A HCA2 2 62955.3928 36.832412523 0.000759396<br>HCA2 HCA2 2 29962.4608 41.58004158 0.000212547<br>
;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)<br>;D = A, B = 1/P, C = E<br><br>and in the default directive of the forcefield.itp i made the following changes <br> [ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>2 1 no 0.0 0.0<br><br>what values should i give for the sigma and epsilon in the [ atomtype ] directive and pairtypes directive . if i ignore the pair types it giving error no default Lj 1-4 interactions. though i am using nbfun as 2 to use the buckingham potential. I have only the values of the A,B,C. How to get sigma and epsilon if they are required. <br>
Did i modify the ffnonbonded.itp in the correct manner ? or any thing went wrong?<br> <br>please help me in this regard.<br><br>Thank you in advance.<br><br>
Regards,<br>Ramesh. <br></div>