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MARTINI and GROMACS 4?
- robraunjp
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13 years 9 months ago #383
by robraunjp
MARTINI and GROMACS 4? was created by robraunjp
Hello
I starded using MARTINI with GROMACS 3.3, but moved to GROMACS 4. I did have some problems when using MARTINI with GROMACS 4. For instance: the forcefield itp files were not recognized when called by a top file. To solve that, I pasted the entire content of martini.itp, martini_ions.itp and martini_aminoacids.itp onto the top file and it worked.
Is that OK?
Am I missing some (very obvious) aspects of top file structure of GROMACS4 that differ from previous GROMACS versions?
Thanks
I starded using MARTINI with GROMACS 3.3, but moved to GROMACS 4. I did have some problems when using MARTINI with GROMACS 4. For instance: the forcefield itp files were not recognized when called by a top file. To solve that, I pasted the entire content of martini.itp, martini_ions.itp and martini_aminoacids.itp onto the top file and it worked.
Is that OK?
Am I missing some (very obvious) aspects of top file structure of GROMACS4 that differ from previous GROMACS versions?
Thanks
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- Justin
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13 years 9 months ago #385
by Justin
Replied by Justin on topic MARTINI and GROMACS 4?
"the forcefield itp files were not recognized when called by a top file."
For me, the Gromacs 4.02, 4.03 and 4.07 all work when the itp files are simply included in the .top file: #include "martini_v2.1.itp ".
For me, the Gromacs 4.02, 4.03 and 4.07 all work when the itp files are simply included in the .top file: #include "martini_v2.1.itp ".
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- robraunjp
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13 years 8 months ago #391
by robraunjp
Replied by robraunjp on topic MARTINI and GROMACS 4?
I sorted it out. My problem was with "Invalid order for directive defaults". As seen at
www.gromacs.org/Documentation/Errors#Inv...r_directive_defaults
I had something like
#include "topol_A.itp"
#include "topol_B.itp"
#include "ligand.itp"
#ifdef POSRES
#include "posre_A.itp"
#include "posre_B.itp"
#include "ligand_posre.itp"
#endif
when I should be using
#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp"
#endif
#include "topol_B.itp"
#ifdef POSRES
#include "posre_B.itp"
#endif
#include "ligand.itp"
#ifdef POSRES
#include "ligand_posre.itp"
#endif
Thank you anyway :)
I had something like
#include "topol_A.itp"
#include "topol_B.itp"
#include "ligand.itp"
#ifdef POSRES
#include "posre_A.itp"
#include "posre_B.itp"
#include "ligand_posre.itp"
#endif
when I should be using
#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp"
#endif
#include "topol_B.itp"
#ifdef POSRES
#include "posre_B.itp"
#endif
#include "ligand.itp"
#ifdef POSRES
#include "ligand_posre.itp"
#endif
Thank you anyway :)
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