On 16/06/2011 7:59 PM, Netaly Khazanov wrote:
Hi,
My system is protein +DNA.
I am trying to perform implicit solvent calculation using Amber 99.
In the begging I wanted to minimize the system and got this error message.
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s) missing or negative for atom type 'N*'
GB parameter(s) missing or negative for atom type 'CM'
GB parameter(s) missing or negative for atom type 'P'
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: grompp.c, line: 1123
Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 5 atomtypes or they might be
negative.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
All the atoms, in which parametres are missing belong to DNA.
Should I add them manually to gbsa.itp? ( but i don't know the right
parameters?).
I expect you're going to have to check in the literature whether such
parameters exist. Unfortunately, not every combination of everything can
be available in a nice shrink-wrapped package :) Once you've found them,
then you'll have to fill in the columns of the above-mentioned section
accordingly.
Mark
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