On 12/11/12 4:30 PM, Hovakim Grabski wrote:
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:


Atomtypes are case-sensitive, so "OS" and "os" are not, in fact, the same atom 
type.


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?

Yes, but you'll need to post the contents of the .itp files if you want feedback. Chapter 5 of the manual explains the required order. Force-field level directives ([defaults], [atomtypes], etc) need to precede the declaration of any [moleculetype] block. From the above fatal error, you are not satisfying this requirement.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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