[gmx-users] Solvating Podophyllotoxin in ethanol

[Justin Lemkul]

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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