[gmx-users] To modify PRODRG-generated .itp file?

Yun Shi yunshi09 at gmail.com
Thu Aug 11 00:03:15 CEST 2011

Hi all,

In addition to modifying atomic charges to the .itp file generated by
PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4
LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ
interactions) with the vdw C12 and C6 parameters I prefer.

So should I just make changes to the [ pairs ] section of the .itp file? For
example, change

; ai  aj  fu    c0, c1, ...
   1   4   1


; ai  aj  fu    c0, c1, ...
   1   4   1   0.004724   1.84e-6

How can I make sure it will override the parameters in the [ pairtypes ]
section of the ffnonbonded.itp file? And I should make these values (c0 for
C6, c1 for C12) in accordance with the units in [ pairtypes ] section,

Moreover, I want to change some dihedral parameters. But I saw the .itp file
generated by PRODRG as something like

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
10   5   4   3   1      0.0    5.9 3      0.0    5.9 3

so 0.0 is the phase shift, 5.9 is the force constant, 3 is the multiplicity,
but why these values appeared twice in a row? When I modify them, should I
also write them twice as this format? Will it override dihedral parameters
that are already in the ffbonded.itp file?

Thanks very much,

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