[gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2

[Berk Hess]

Hi,

Note that grompp prints the atomtype that causes the problems.

You should copy the last line of share/top/charmm27.ff/gb.itp and rename MCH3 to MCH3S.
I have fixed this for 4.5.3 and I have also made the grompp error messages clearer.

Berk

From: zhngbn at gmail.com
To: gmx-users at gromacs.org
Date: Wed, 3 Nov 2010 21:23:33 -0700
Subject: [gmx-users] charmm27 force filed bug for MET residue with vsites in	gromacs 4.5.2 

Dear all:
I used gromacs 4.5.2 to generate the topology for a small protein with charmm27.pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter -p topol -nochargegrp
When I try to use the topology in grompp, the following error appeared: Fatal error:Can't do GB electrostatics; the forcefield is missing 1 values foratomtype radii, or they might be negative
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:  No default Constr. No Conn. types (between atom 181 and 182)
This problem does NOT show up in 4.5.1.
Thanks,Bin

========================================
   171        NH1     15    MET      N    171      -0.47     15.015   ; qtot 1.53    172          H     15    MET     HN    172       0.31          0   ; qtot 1.84    173        CT1     15    MET     CA    173       0.07     13.019   ; qtot 1.91    174         HB     15    MET     HA    174       0.09          0   ; qtot 2   175        CT2     15    MET     CB    175      -0.18     14.027   ; qtot 1.82    176         HA     15    MET    HB1    176       0.09          0   ; qtot 1.91    177         HA     15    MET    HB2    177       0.09          0   ; qtot 2   178        CT2     15    MET     CG    178      -0.14     14.027   ; qtot 1.86    179         HA     15    MET    HG1    179       0.09          0   ; qtot 1.95    180         HA     15    MET    HG2    180       0.09          0   ; qtot 2.04    181          S     15    MET     SD    181      -0.09      32.06   ; qtot 1.95    182      MCH3S     15    MET   MCE1    182          0     7.5175   ; qtot 1.95    183      MCH3S     15    MET   MCE2    183          0     7.5175   ; qtot 1.95    184        CT3     15    MET     CE    184      -0.22          0   ; qtot 1.73    185         HA     15    MET    HE1    185       0.09          0   ; qtot 1.82    186         HA     15    MET    HE2    186       0.09          0   ; qtot 1.91    187         HA     15    MET    HE3    187       0.09          0   ; qtot 2   188          C     15    MET      C    188       0.51     12.011   ; qtot 2.51    189          O     15    MET      O    189      -0.51     15.999   ; qtot 2

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