<p>Hello,</p><p>I try to perform an implicit solvent simulation with Gromacs
4.5.3. version. I have a system corresponding to 6 peptides generated by Pymol
with simmetrical cell, so I have a single PDB. I used OPLS-AA and i put the
N-and C- termini as NH2 and COOH. My topology file is correct, and is all
systems are included.</p><p>; Include forcefield parameters<br />#include
"./oplsaa.ff/forcefield.itp" -------> in this .itp file is included
gbsa.itp<br /><br />; Include chain topologies<br />#include
"topol_Protein_chain_A.itp"<br />#include
"topol_Protein_chain_B.itp"<br />#include
"topol_Protein_chain_C.itp"<br />#include
"topol_Protein_chain_D.itp"<br />#include
"topol_Protein_chain_E.itp"<br />#include
"topol_Protein_chain_F.itp"<br /><br />; Include water topology<br
/>#include "./oplsaa.ff/tip3p.itp"<br /><br />#ifdef POSRES_WATER<br
/>; Position restraint for each water oxygen<br />[ position_restraints ]<br
/>; i funct fcx fcy fcz<br /> 1 1 1000
1000 1000<br />#endif<br /> <br />; Include topology for ions<br
/>#include "./oplsaa.ff/ions.itp"<br /><br />[ system ]<br />; Name<br
/>Protein<br /><br />[ molecules ]<br />; Compound #mols<br
/>Protein_chain_A 1<br />Protein_chain_B 1<br />Protein_chain_C 1<br
/>Protein_chain_D 1<br />Protein_chain_E 1<br />Protein_chain_F 1<br
/>-----------------------------------------------------------------------------</p><p>When
I start my simulations (md_start.mdp) in implicit solvent, i have this fatal
error:</p><p>GB parameter(s) missing or negative for atom type 'opls_912B'<br
/><br />GB parameter(s) missing or negative for atom type 'opls_267'<br /><br
/>GB parameter(s) missing or negative for atom type 'opls_269'<br /><br />GB
parameter(s) missing or negative for atom type 'opls_268'<br /><br />GB
parameter(s) missing or negative for atom type 'opls_270'</p><p>Program grompp,
VERSION 4.5.3<br />Source code file: grompp.c, line: 1123<br /><br />Fatal
error:<br />Can't do GB electrostatics; the implicit_genborn_params section of
the forcefield is missing parameters for 5 atomtypes or they might be
negative.<br />For more information and tips for troubleshooting, please check
the GROMACS<br />website at
http://www.gromacs.org/Documentation/Errors.</p><p>----------------------------------------------------------------------------</p><p>Controlling
these atoms they corresponding to:</p><p>opls_912B= the CA of N-terminal
residue </p><p>opls_267= Co in COOH</p><p>opls_268= Oh in COOH </p><p>opls_269=
Oc in COOH neutral</p><p>opls_270= H in
COOH</p><p>----------------------------------------</p><p>in the file gbsa.itp
in opls.ff directory these atoms missing. Now, have I done something wrong? If
is all ok, is it possible to create these missing atoms in the gbsa.itp
file?</p><p>thanx,</p><p>francesca stanzione</p>