[gmx-users] protein constrained, ligand ot constrained

[mollica.luca at hsr.it]

Dear all,
I would like to set up a simulation of a protein-ligand system with the
protein left bond-constrained using LINCS algorithm and the ligand left
unconstrained, i.e. in order to check the effect of some variations of
force constants that I have computed on the protein-ligand interactions.
Do you have any suggestion about this issue ?
Actually, the only solution that I have (as suggested by someone else,
also) is to use the mdp option

constraints    =   none

and write a new section for the protein topology of this kind (values
are w/o meaning):

[constraints]

1 2 1 0.150
1 3 1 0.179
2 9 1 0.130

etc etc ... an almost simple script could do the job.
This method seems to me, by now, the right one, but do you know any
other more straightforward method for performing this operation ?

Thanx in advance

Luca



********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
www.5xmille.org