[gmx-users] simulation in implicit solvent for non standar residues

Rebeca García Fandiño regafan at hotmail.com
Wed Nov 12 13:35:55 CET 2014


I am trying to do a MD
simulation in GROMACS of two non standar molecules  using implicit solvent. Using explicit
solvent I could do the simulation without problem using AMBER-GAFF or CHARMM-CGenFF
parameters. To prepare the simulation in implicit solvent, I can see in the
manual that a section in the topology has to be introduced to list the

implicit_genborn_params ]

Using the gbsa.itp
default files in GROMACS, when I try to do grompp, I get errors related to “GB parameter(s) missing or
negative for atom type 'XX' “, as it is logical, since the GAFF or CGenFF
parameters are not included in the default gbsa.itp file.

I have read the mailing list about obtaining
parameters for the section [ implicit_genborn_params ], and in general, what it
is recommended is to use the parameters for similar atoms. Is there any other
more exhaustive way of taking these parameters?What happens with the parameters for different atoms not included in gbsa.itp?

Besides, also in relation with MD simulations
in implicit solvent, I have another question.  I have
also read about it in the mailing list and it is still confusing for me. If the system is
charged, is it not a problem for carrying out the simulation? Is there a way to
neutralize the system?
Thanks a lot for your help in advance.
Best wishes,
Dra. Rebeca GarciaSantiago de Compostela UniversitySpainregafan at hotmail.com


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