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? Thank you. Best regards, Changwoon Jang On Mon, Jan 25, 2016 at 1:34 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > See > http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx > > Mark > > On Mon, 25 Jan 2016 19:19 Chang Woon Jang <changwoonj...@gmail.com> wrote: > > > Dear Gromacs Users, > > > > I have two types of molecules. The topology file was separated by one > > (topol.top) and two (DGA.itp, and J230.itp). > > > > The format I made in topol.top is > > > > #include "DGA.itp" > > #include "J230.itp" > > > > [ system ] > > ; Name > > DGA and J230 > > > > [ molecules ] > > ; Compound #mols > > Other_chain_A 200 > > Other_chain_B 100 > > > > In the DGA.itp and J230.itp files, I formatted like but only difference > > between DGA.itp and J230.tip is type (C and D) and mass. > > > > > > [ defaults ] > > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > > 1 1 no 0.0 0.0 > > [ atomtypes ] > > ; type mass charge ptype sigma epsilon > > B 42.090999 0.000 A 1.0000 1.0000 > > A 151.185798 0.000 A 1.0000 1.0000 > > > > [ molecuetype ] > > Other_chain_A 3 > > > > [atoms] > > ; nr type resnr residue atom cgnr charge mass > > 1 A 1 RES A1 1 0.00000 151.185798 > > 2 A 1 RES A2 2 0.00000 151.185798 > > 3 B 1 RES B1 3 0.00000 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 > > > > An error says, > > > > Fatal error: > > Syntax error - file DGA.itp, line 1 > > Last line read: > > ' [ defaults ]' > > invalid order for directive moleculetype > > For more ..... > > > > > > I am trying to simulate a Coarse-grained model and the topology file was > > created. I think that the formatting is correct following an example from > > votca coarse graining tool. When I use two type of molecules in atomistic > > scale, these separated topology files work fine. > > > > Would you please what the correct format of this to be run? > > > > Thank you very much for your advise. > > > > > > Best regards, > > Changwoon Jang, > > -- > > 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-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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