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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