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

[Mark Abraham]

On 21/06/2011 4:15 PM, bharat gupta wrote:
> I fixed it ... but now after using the command : grompp -f em.mdp -c 
> solv.gro -p topol.top -o ions.tpr
>
> I am getting a charge of  -9.999971e-01
>
>
> Since the charge has to be in whole number, what shall I do in this 
> case. (The ligand that I am using is phosphotyrosine)

OK, that's what I expected you were doing - truncating the output and 
not rounding appropriately. See 
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic again - 
I've updated it to deal with this issue more explicitly.

Mark

>
> On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 21/06/2011 3:03 PM, bharat gupta wrote:
>
>         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
>         -------------------------------------------------------
>
>
>     You have to make an attempt to solve your own problems :-) We have
>     better things to do than oversee every move you make. Follow that
>     link and read about this issue.
>
>
>     Mark
>     -- 
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>
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
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