[gmx-users] Re: Error during executing the protein ligand tutorial

[bharat gupta]

Now I changed the .top file in this way and I am getting this error now :-

change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

;Include ligand topology
#include "PTR.itp"

[ moleculetype ]
; Name            nrexcl
Protein_chain_A     3

=====================

error:-


Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 23220 of the 23220 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 20092 of the 23220 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype LIG
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)





On Tue, Jun 21, 2011 at 1:56 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 21/06/2011 2:51 PM, bharat gupta wrote:
>
>> ok now I am doing the things again and here is the result of output of
>> each command till adding ions. At the time of executing the command grompp
>> for reading em.mdp file for ions.tpr generation, I am getting the following
>> error:-
>>
>>
>> Fatal error:
>> Syntax error - File PTR.itp, line 7
>> 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<http://www.gromacs.org/Documentation/Errors>
>> ------------------------------**-------------------------
>>
>> "Everything's formed from particles" (Van der Graaf Generator)
>>
>> here's a list of output , I obtained till the step of adding ion ??
>>
>
> You haven't followed the steps of the tutorial well enough. Specifically,
> you've edited a .top or .itp file in the wrong place.
>
> Mark
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
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