[gmx-users] Error - syntax

[Justin Lemkul]

On 1/25/16 2:50 PM, Chang Woon Jang wrote:
> Dear Mark,
>
>     Thank you for the information. I have changed the topol.top file now like
>
> I put another three lined for posres right below each itp, DGA.itp and
> J230.itp.
>
> ; Include forcefield parameters
> ;#include "forcefield.itp"
>
> ; Include chain topologies
> #include "DGA.itp"
> #ifdef POSRES
> #include "porse_A.itp"
> #endif
>
> #include "J230.itp"
> #ifdef POSRES
> #include "porse_B.itp"
> #endif
>
> [ system ]
> ; Name
> Built with Packmol
>
> [ molecules ]
> ; Compound        #mols
> Other_chain_A       200
> Other_chain_B       100
>
>
>     In the DGA.itp file,
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>    1             1               no              0.0     0.0
>
> [ atomtypes ]
> ;type    mass    charge       ptype          sigma      epsilon
>   B     42.080999  0.000       A        1.000000000  1.000000000
>   A     151.18579  0.000       A        1.000000000  1.000000000
>
> [ moleculetype ]
> Other_chain_A 3
>
> [atoms]
> ; nr type resnr residue atom cgnr charge mass
> 1 A 1 RES A1 1 0.000000 151.18579
> 2 A 1 RES A2 2 0.000000 151.18579
> 3 B 1 RES B1 3 0.000000 42.080999
>
>
> [ bonds ]
> 1 3   8   1 1.0; 1:bond:1
> 2 3   8   1 1.0; 1:bond:2
>
> [ angles ]
> 1 3 2   8  1 1.0  ; 1:angle:1
>
>
>
> In J230.itp file,
>
> [ atomtypes ]
> ;type    mass    charge       ptype          sigma      epsilon
>   D     100.16139  0.000       A        1.000000000  1.000000000
>   C     74.103099  0.000       A        1.000000000  1.000000000
>
> [ moleculetype ]
> Other_chain_B 3
>
> [atoms]
> ; nr type resnr residue atom cgnr charge mass
> 1 C 1 RES C1 1 0.000000 74.103099
> 2 D 1 RES D1 2 0.000000 100.16139
> 3 C 1 RES C2 3 0.000000 74.103099
>
>
> [ bonds ]
> 1 2   8  1  1.0  ; 1:bond:1
> 2 3   8  1  1.0  ; 1:bond:2
>
> [ angles ]
> 1 2 3   8   1  1.0 ; 1:angle:1
>
>
> The error still occurred as follow.
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
> Source code file:
> /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/gmxpreprocess/topio.c,
> line: 727
>
> Fatal error:
> Syntax error - File J230.topfile.itp, line 5
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> Don't I understand the passage correctly you linked?
>

Spend some time reading Chapter 5 of the manual.  You have to declare all force 
field-level directives before you can declare molecule-level directives.  The 
parser has to know everything about the form of the force field before you can 
start building molecules within that force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================