[gmx-users] QMMM grompp error atom numbers fields.

Groenhof, Gerrit ggroenh at gwdg.de
Wed May 25 08:24:23 CEST 2016


this is weird. I assume you've put the *'s only in your email?

Could you send me (off list) the mdp, index, top and gro file? Perhaps something else, such as missing link atom triggers the error message incorrectly.


Subject: [gmx-users] QMMM grompp error atom numbers fields.
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Dear members,

I am trying to run a QMMM simulation  in Gromacs4.5.5 using amber99sb-ILDN
together with orca. When I tried to run grompp I obtain the following error:

*  It appears as if you are trying to run a QM/MM calculation, but the
force  field you are using does not contain atom numbers fields. This is
an  optional field (introduced in Gromacs 3.3) for general runs, but
mandatory  for QM/MM. The good news is that it is easy to add - put the
atom number as  an integer just before the mass column in ffXXXnb.itp.  NB:
United atoms have the same atom numbers as normal ones.*

When I go through the forcefield itp file at
share/top/amber99sb-ildn.ff/ffnonbonded.itp I have seen that this
forcefield has an atom number column, or at least I have understood that it

[ atomtypes ]
; name      *at.num*  mass     charge ptype  sigma      epsilon
Br          *35*      79.90    0.0000  A   0.00000e+00  0.00000e+00
C           * 6 *     12.01    0.0000  A   3.39967e-01  3.59824e-01
CA           *6*      12.01    0.0000  A   3.39967e-01  3.59824e-01
CB       *    6 *     12.01    0.0000  A   3.39967e-01  3.59824e-01
CC           *6 *     12.01    0.0000  A   3.39967e-01  3.59824e-01

The 'at. num' column is the atom number? If it is, how can I solve this
error? Could you help me with that?

Thanks in advance,

Melchor Sanchez-Martinez

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