On 2/06/2012 7:10 PM, xi zhao wrote:
Dear gmx-users:
When I try to simulation a system: protein + ligand molecule using the
Implicit Solvent method. the parameters of Ligand were produced by
acpype, but when grompped, the appeared"
" Velocities were taken from a Maxwell distribution at 300 K
GB parameter(s) missing or negative for atom type 'o'
GB parameter(s) missing or negative for atom type 'os'
GB parameter(s) missing or negative for atom type 'c'
GB parameter(s) missing or negative for atom type 'c3'
GB parameter(s) missing or negative for atom type 'hc'
GB parameter(s) missing or negative for atom type 'h1'
-------------------------------------------------------
Program grompp_d, VERSION 4.5.3
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 6 atomtypes or they might be
negative."
when I modified "4
<http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>amber99sbr.ff/gbsa.itp
by adding the atomtype of ligand, the problem is still the same,
Then you apparently didn't add them correctly. See manual section 5.3.5
and second paragraph of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Mark
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