[gmx-users] Question

[Eric Smoll]

Thanks for the guidance, Justin.

-Eric

On Thu, Oct 23, 2014 at 2:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/23/14 4:29 PM, Eric Smoll wrote:
>
>> Hello Gromacs users,
>>
>> If I have all the files that were used to generate a trajectory file, what
>> is the proper procedure to update the atomnames in the trajectory. My best
>> guess is below. Is this problematic?
>>
>> # remove first frame of trajectory
>> cat << EOF > tmp.ndx
>> [ FIRSTFRAME ]
>> 1
>> EOF
>>
>> trjconv -fr tmp.ndx -f old.trr -s old.tpr -o tmp.gro
>>
>> # Edit tmp.gro and rename edit.gro
>>
>> # Edit old.itp to edit.itp
>>
>> # Edit old.top tp edit.top
>>
>> grompp -f old.mdp -c edit.gro -p edit.top -o edit.tpr
>>
>> trjconv -s edit.tpr -f old.trr -o new.trr
>>
>>
> Why do you need new atom names?  Since atom names are not stored in the
> trajectory, it is simple to change the input to have things reinterpreted:
>
> 1. Edit topology that contains atom names to be changed.
> 2. Run grompp with original coordinate file, new topology, and -maxwarn 1
> (because it will complain about mismatching atom names, but will override
> those in the coordinate file with whatever is in the topology)
> 3. Carry out whatever analysis you wanted with the new atom names
> 4. Profit?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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