[gmx-users] Ligand moves out of box during EM steps

[Alberto Malvezzi]

Hi Nataraj,
this happened to me also.
When you make an energy minimization, gromacs alters the coordinates of 
your protein. When you place the ligand back to the gro file, it will be 
placed far from its site. To solve this problem I take the original 
complex and fit it to the minimized protein (using DeepView or any other 
program like Whatif, for example), then save only the ligand of the 
complex and use these new coordinates to feed the gro file of the 
minimized protein.
Hope I understood your problem.
All the best
Alberto

raja wrote:

>Dear Tsjerk,
>          Thanks for your prompt replies, But please bit elaborate your
>          answer. Yea I do use editconf
>for the purpose of  renumbering ligand after pasted in original protein
>gro file produed by pdb2gmx step (as per my previous mail). But where
>come the option of -s in ediconf as you mentioned in your earlier mail
>".... If you place your ligand (-s first atom)". 
>
>Please mention the exact command to position the ligand in its original
>place using editconf. More I would like to add more observation , during
>the process of these preparation of protein-enzyme complex, upto grompp
>for em file, the added ligand atoms are appears to be distorted but at
>the end of the energy minimization, the original molecules of ligand is
>restored.(may be this is not my concern rightnow,so please give me
>elaborate command to position the ligand in its active site)
>
>With thanks !
>B.Nataraj
>
>
>On Wed, 22 Mar 2006 14:31:42 +0100, "Tsjerk Wassenaar"
><tsjerkw at gmail.com> said:
>  
>
>>Hi Raja,
>>
>>When you generate a .tpr file (for whatever purpose) all molecules will
>>be
>>mapped to a rectangular box as good as possible. For this, the first atom
>>of
>>the molecule is used. So when a molecule happens to be sticking out of
>>the
>>rectangular box, or when it is just pushed over the border during EM/PR,
>>it
>>will be mapped to the other side and it will appear to have jumped. If
>>you
>>place your ligand (-s first atom) in the center of the rectangular box
>>(editconf -c), it will stay there during EM/PR.
>>
>>Cheers,
>>
>>Tsjerk
>>
>>On 3/22/06, raja <raja_28 at fastmail.us> wrote:
>>    
>>
>>>Dear Tsjerk,
>>>        Thanks for your reply. But I have not gone to the stage of
>>>        dynamics yet. I am still struck at energy minimization. Now
>>>        atleast I could reason out why it happens, but I dont know how
>>>        to stop it. The reason is everytime
>>>when I convert ligand-enzyme complex using pdb2gmx, I trim off the
>>>ligand and convert the protein part alone, later I
>>>paste the drug molecule in the resultant file. I suspect that could be
>>>the problem,so I try to fix it by myself.
>>>
>>>With thanks !
>>>B.Nataraj
>>>On Wed, 22 Mar 2006 07:54:05 +0100, "Tsjerk Wassenaar"
>>><tsjerkw at gmail.com> said:
>>>      
>>>
>>>>Hi Raja,
>>>>
>>>>Probably PBC. Nothing wrong, just visual. You can try to center your
>>>>system
>>>>on the ligand before starting the simulation, which should keep it "in
>>>>place".
>>>>
>>>>Tsjerk
>>>>
>>>>On 3/22/06, raja <raja_28 at fastmail.us> wrote:
>>>>        
>>>>
>>>>>Dear GMXIONS,
>>>>>I reposting the same query since not getting response for my previous
>>>>>posting. In short
>>>>>I am unable to restraint the ligand at its active site during
>>>>>minimization, though I used position restrints
>>>>>for all of the atom types of my ligand. At the end of simulation, it
>>>>>          
>>>>>
>>>is
>>>      
>>>
>>>>>jumping out of active site and located
>>>>>itself at the corner of the water box.
>>>>>
>>>>>Kindly provide me the solution to retain the ligand at its original
>>>>>position during minimization step!
>>>>>
>>>>>
>>>>>With thanks !
>>>>>B.Nataraj
>>>>>
>>>>>
>>>>>
>>>>>--
>>>>>  raja
>>>>>  raja_28 at fastmail.us
>>>>>
>>>>>--
>>>>>http://www.fastmail.fm - Email service worth paying for. Try it for
>>>>>          
>>>>>
>>>free
>>>      
>>>
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>>>>>          
>>>>>
>>>>
>>>>--
>>>>
>>>>Tsjerk A. Wassenaar, M.Sc.
>>>>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>>>>Dept. of Biophysical Chemistry
>>>>University of Groningen
>>>>Nijenborgh 4
>>>>9747AG Groningen, The Netherlands
>>>>+31 50 363 4336
>>>>        
>>>>
>>>--
>>>  raja
>>>  raja_28 at fastmail.us
>>>
>>>--
>>>http://www.fastmail.fm - Email service worth paying for. Try it for free
>>>
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>>>      
>>>
>>
>>--
>>
>>Tsjerk A. Wassenaar, M.Sc.
>>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>>Dept. of Biophysical Chemistry
>>University of Groningen
>>Nijenborgh 4
>>9747AG Groningen, The Netherlands
>>+31 50 363 4336
>>    
>>