[gmx-users] Error - syntax
Justin Lemkul
jalemkul at vt.edu
Mon Jan 25 20:54:27 CET 2016
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
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