<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
Hi,<br><br>Note that grompp prints the atomtype that causes the problems.<br><br>You should copy the last line of share/top/charmm27.ff/gb.itp and rename MCH3 to MCH3S.<br>I have fixed this for 4.5.3 and I have also made the grompp error messages clearer.<br><br>Berk<br><br><hr id="stopSpelling">From: zhngbn@gmail.com<br>To: gmx-users@gromacs.org<br>Date: Wed, 3 Nov 2010 21:23:33 -0700<br>Subject: [gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2 <br><br><div>Dear all:</div><div><br></div><div>I used gromacs 4.5.2 to generate the topology for a small protein with charmm27.</div><div>pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter -p topol -nochargegrp</div><div><br></div><div>When I try to use the topology in grompp, the following error appeared: </div><div>Fatal error:</div><div>Can't do GB electrostatics; the forcefield is missing 1 values for</div><div>atomtype radii, or they might be negative</div><div><br></div><div>I was able to isolate the atom that's causing the problem, which is MCH3S in the Met residue (as shown in the attached segment of the topology). It was named MCH3 as in gromacs 4.5.1. However, if I rename the atom, then another error occurs:</div><div> No default Constr. No Conn. types (between atom 181 and 182)</div><div><br></div><div>This problem does NOT show up in 4.5.1.</div><div><br></div><div>Thanks,</div><div>Bin</div><div><br></div><div><br></div><div>========================================</div><div><br></div><div> 171 NH1 15 MET N 171 -0.47 15.015 ; qtot 1.53 </div><div> 172 H 15 MET HN 172 0.31 0 ; qtot 1.84 </div><div> 173 CT1 15 MET CA 173 0.07 13.019 ; qtot 1.91 </div><div> 174 HB 15 MET HA 174 0.09 0 ; qtot 2</div><div> 175 CT2 15 MET CB 175 -0.18 14.027 ; qtot 1.82 </div><div> 176 HA 15 MET HB1 176 0.09 0 ; qtot 1.91 </div><div> 177 HA 15 MET HB2 177 0.09 0 ; qtot 2</div><div> 178 CT2 15 MET CG 178 -0.14 14.027 ; qtot 1.86 </div><div> 179 HA 15 MET HG1 179 0.09 0 ; qtot 1.95 </div><div> 180 HA 15 MET HG2 180 0.09 0 ; qtot 2.04 </div><div> 181 S 15 MET SD 181 -0.09 32.06 ; qtot 1.95 </div><div><font class="ecxApple-style-span" color="#1e00fb"> 182 MCH3S 15 MET MCE1 182 0 7.5175 ; qtot 1.95 </font></div><div><font class="ecxApple-style-span" color="#1e00fb"> 183 MCH3S 15 MET MCE2 183 0 7.5175 ; qtot 1.95 </font></div><div> 184 CT3 15 MET CE 184 -0.22 0 ; qtot 1.73 </div><div> 185 HA 15 MET HE1 185 0.09 0 ; qtot 1.82 </div><div> 186 HA 15 MET HE2 186 0.09 0 ; qtot 1.91 </div><div> 187 HA 15 MET HE3 187 0.09 0 ; qtot 2</div><div> 188 C 15 MET C 188 0.51 12.011 ; qtot 2.51 </div><div> 189 O 15 MET O 189 -0.51 15.999 ; qtot 2</div><div><br></div><br>--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists </body>
</html>