[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

[Mark Abraham]

On 17/06/2011 12:33 AM, maria goranovic wrote:
> thought of that, but the trajectory also has HISB data .. 

.xtc and .trr trajectories have no atom identification. That's why lots 
of the tools require a .tpr or coordinate file, together with a 
trajectory file in order to function. Using bash, look at gmxdump -f 
traj.xtc 2>&1|less to learn what is there. You merely need to be 
confident the atom ordering hasn't changed from whatever generated the 
old trajectory.

> so I guess I will have to alter it frame by frame ?

Even if your trajectory is some pseudo-format like .pdb or .gro, you can 
convert it back to one of the above easily.

Mark

> On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 16/06/2011 11:01 PM, maria goranovic wrote:
>
>         Hi
>
>         I had a simulation run with 4.0.7, using opls-aa for a protein
>         in water.
>
>         I now use part of the protein coordinates output from the
>         simulation, and use pdb2gmx as:
>
>         pdb2gmx -f conf.gro -ff oplsaa -ignh
>
>         pdb2gmx complains that it cannot find HISB. I checked that the
>         topology files in 4.5.3 do not contain HISB, while those in
>         4.0.7 do.
>
>         It does not suffice to create another copy of the HISE
>         topology in the .rtp file and call it HISB, because a number
>         of hydrogen atoms also have been renamed?
>
>         What can be done? I want to use 4.5.3 because I would prefer
>         to retain residue numbering
>
>
>     Rename all the HISB residues in your input coordinate file to
>     whatever OPLS/AA wants.
>
>     Mark
>     -- 
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>
>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen

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