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

[Justin A. Lemkul]

Yun Shi wrote:
> 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                                          
> 
> to
> 
> ; 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 

You can always verify the contents of the topology using gmxdump on the .tpr 
file produced from it.

> for C6, c1 for C12) in accordance with the units in [ pairtypes ] 
> section, right?
> 

Yes, use correct units.

> 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 

When two sets of values are present, they correspond to the A state and B state 
for free energy calculations.  If you're not doing anything with the free energy 
code, the second set is ignored.

> modify them, should I also write them twice as this format? Will it 
> override dihedral parameters that are already in the ffbonded.itp file?
> 

It should, yes.  But again, use gmxdump to be sure you're getting what you think 
you should be.

-Justin

-- 
========================================

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

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