[gmx-users] trjcat set timestep/amb2gmx?

[Justin Lemkul]

On 4/16/13 5:32 AM, Steven Neumann wrote:
> Thank you all.
>
> Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
> anything like this - basically I wish to convert top.prmtop to top.tpr.
>
>

You will not be able to produce a .tpr file directly.  The amb2gmx script simply 
converts the prmtop to a .top file, which can then be input into grompp.

-Justin

>
>
> On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri
> <francesco.oteri at gmail.com>wrote:
>
>> Hi,
>> yes Marc you are right but the last time I used gromacs on a namd
>> trajectory
>> I noticed that time in the output files is useless 'cause it is always 0.
>> I understand that, since this information is usually took from .trr or
>> .xtc, it cannot
>> be extracted from a .dcd, but it could be more useful using as x the frame
>> number.
>> This could, at least, permitting to visualize the plot with xmgrace without
>> postprocessing
>> the .xvg
>>
>>
>>
>> Francesco
>>
>>
>> 2013/4/16 Mark Abraham <mark.j.abraham at gmail.com>
>>
>>> On Apr 15, 2013 6:27 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 4/15/13 12:23 PM, Steven Neumann wrote:
>>>>>
>>>>> Dear Gmx Users,
>>>>>
>>>>> I obtained dcd trajectory from simulation in another software. I wish
>> to
>>>>> merge many trajectories using trjcat with a proper timestep. Is that
>>> option
>>>>> possible using gromacs or shall use a script to produce tpr file from
>> my
>>>>> prmtop file e.g. amb2gmx ? Any links for such a script?
>>>>>
>>>>
>>>> If you linked against VMD libraries when installing, Gromacs can handle
>>> any trajectory/coordinate file format that VMD can, thus requiring no
>>> conversion. If you need a .tpr file to do the analysis you are trying to
>>> do, then yes, you need to convert topology information into the proper
>>> format.
>>>
>>> ...and be aware that a -s option that accepts both .tpr and (say) .gro
>>> formats (as shown in g_tool -h) might succeed with the latter if only
>> atom
>>> names, rather than (say)  bonding connectivity is required for g_tool to
>>> work.
>>>
>>> Mark
>>>> -Justin
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Research Scientist
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>>
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at
>>> 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
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> 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
>>>
>>
>>
>>
>> --
>> Cordiali saluti, Dr.Oteri Francesco
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> 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
>>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================