<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi!<div><br></div><div>Thanks for pointing this out.</div><div>It is unfortunate that they are missing from the gbsa.itp-file. I will add them, but I do not have time today.</div><div>If you want to get going, you can add them yourself. </div><div>The gb-parameters are essentially based on atom hybridization, so for each missing atom you find another that has the same (sp, sp2,sp3) hybridization, and add it to the gbsa.itp-file.</div><div><br></div><div>Cheers</div><div>/Per</div><div><br><div><div>21 jan 2011 kl. 13.51 skrev <a href="mailto:francesca.stanzione@unina.it">francesca.stanzione@unina.it</a>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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
<a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a>.</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>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></body></html>