[gmx-users] pdb2gmx error

[Acoot Brett]

Hi Mark,
 
The fifth residue of Chain A is Asn, not Val. But Asn also no CG.
 
Acoot
 

________________________________
 From: Acoot Brett <acootbrett at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 2 April 2012 10:48 AM
Subject: Re: [gmx-users] pdb2gmx error
  

Hi Mark,
 
I have renumbered the residues. Both 2 chains start from Resis 1. The pdb2gmx still does not work. The fifth residue in the chain A is Val, no CG atom. The fifth residue of chain B is Gly, no CG atom.
 
What is your suggestion?
 
Cheers,
 
Acoot
________________________________

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 2 April 2012 10:32 AM
Subject: Re: [gmx-users] pdb2gmx error



On 2/04/2012 10:26 AM, Acoot Brett wrote: 
Hi Mark, 
>  
>As for the pdb2gmx is the first step, there is still no gro file and rtp file produced by this step.   
I didn't suggest you look at *output* files.



>
>In addition, in my protein the first residue is Resi 71, which means there is no resi 5 at all.   
The fifth in the sequence, then. Perhaps with a terminal residue.
    After all, you haven't told us anything about what you're doing.

Mark


  
>I am looking forward to getting your suggestion. 
>  
>Cheers, 
>  
>Acoot 
>
> 
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Sent: Monday, 2 April 2012 10:22 AM
>Subject: Re: [gmx-users] pdb2gmx error
>  
>
>On 2/04/2012 10:19 AM, Acoot Brett wrote: 
>Dear All, 
>>
>>I just run a pdb2gmx of a protein, the error message is " 
>>Fatal error:  
>>Atom CG is used in an interaction of type atom in the topology  
>>database, but an atom of that name was not found in residue  
>>number 5." 
>>    
>>According to the sugestion I have tried to find the reason in " 
>>http://www.gromacs.org/Documentation/Errors" 
>>
>>But in that part of Document no this error was explained. 
>>
>>I am looking forward to getting an explaination from you. 
>>  
>Like it says, look at residue 5 in your .gro and .rtp
                input files. They need to match well enough.
>
>Mark
>  
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> 
 
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