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

[bharat gupta]

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)


On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham <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<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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110621/fce953d8/attachment.html>