[gmx-users] Invallid order of atomtypes

[Mark Abraham]

Hi,

You can't define a molecule before you define the force field.

Mark

On Thu, 5 Oct 2017 11:53 Sergio Manzetti <sergio.manzetti at fjordforsk.no>
wrote:

> Hi, I Have an itp file with the given first part:
>
>
> [ moleculetype ]
> ; Name nrexcl
> mols 3
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon
> CR 6 12.0110 0.0 A 0.387541 0.230120
> F 9 18.9984 0.0 A 0.290433 0.564840
> SO2 16 32.0660 0.0 A 0.374177 1.966480
> O2CM 8 15.9994 0.0 A 0.302905 0.502080
>
>
> [ pairtypes ]
> ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
> CR CR 1 0.338541 0.041840
> CR F 1 0.314487 0.153730
> CR SO2 1 0.356359 0.286841
> CR O2CM 1 0.320723 0.144938
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> .....
>
>
> and the top file looks like:
>
> #include "zinc_mols.itp"
> #include "/usr/share/gromacs/top/charmm27.ff/forcefield.itp"
> #include "spc.itp"
>
> [ system ]
> MOLS in water and
>
> [ molecules ]
> ; Compound nmols
> MOLS 201
> SOL 10719
>
>
> However, at grompp I get:
>
> Fatal error:
> Syntax error - File zinc_pfos.itp, line 7
> Last line read:
> '[ moleculetype ]'
> Invalid order for directive moleculetype
>
>
> I have checked
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
>
> but the top file is fine, accordingly
>
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.