[gmx-users] Implicit solvent calculatiom

[Netaly Khazanov]

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?).

Thanks in advance.
Netaly Khazanov.
Post-doctoral student.
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