On 10/17/12 2:31 PM, Albert wrote:
Hello Justine:
I've got the following messages by command:
grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr
Setting gen_seed to 18463
Velocities were taken from a Maxwell distribution at 310 K
GB parameter(s) missing or negative for atom type 'OS'
-------------------------------------------------------
Program grompp, VERSION 4.5.5
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 1 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
-------------------------------------------------------
"Uh-oh .... Right Again" (Laurie Anderson)
You need GB parameters for every atom type in the system. Most protein and
nucleic acid types work out of the box, but if you have a complex system with
some novel molecule in it, you have to add parameters for the atom types that it
uses.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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