[gmx-users] Solvating Podophyllotoxin in ethanol

Hovakim Grabski hovakim_grabski at yahoo.com
Tue Dec 11 22:30:06 CET 2012

Dear Gromacs users,
I've been trying to solvate  Podophyllotoxin in ethanol. I used chimera and acpype to create PPT and I got the .itp and .pdb files.
For ethanol I used http://virtualchemistry.org/molecules/64-17-5/index.php .top and GAFF liquid structure .pdb file.
Since some atomtypes match between PTOX.itp and ETA.itp, I changed atomtypes in PTOX to uppercase and when I try Energy Minimization, I get:

WARNING 1 [file PTOX.itp, line 6]:
  Overriding atomtype OS

WARNING 2 [file PTOX.itp, line 7]:
  Overriding atomtype CA

WARNING 3 [file PTOX.itp, line 8]:
  Overriding atomtype C

WARNING 4 [file PTOX.itp, line 9]:
  Overriding atomtype O

WARNING 5 [file PTOX.itp, line 10]:
  Overriding atomtype OH

WARNING 6 [file PTOX.itp, line 11]:
  Overriding atomtype H1

WARNING 7 [file PTOX.itp, line 12]:
  Overriding atomtype HA

WARNING 8 [file PTOX.itp, line 13]:
  Overriding atomtype HC

WARNING 9 [file PTOX.itp, line 14]:
  Overriding atomtype HO

WARNING 10 [file PTOX.itp, line 15]:
  Overriding atomtype H2

Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations

Program grompp, VERSION 4.5.5
Source code file: /home/john1990/code/gromacs-4.5.5/src/kernel/topio.c, line: 656

Fatal error:
Syntax error - File ETA.itp, line 13
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

This is the order in my topology file:

; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"

;Include PTOX topology
#include "PTOX.itp"

; Include ethanol topology
#include "ETA.itp"

Is there any way to fix it?
Thanks in advance,
Best regards,
Hovakim Grabski
Russian-Armenian(Slavonic) University

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