From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 21 2006 - 20:17:10 CDT
Hi Miro,
I had a look at the proline issue. I cannot seem to get autopsf to
remove the hydrogens and re-add them by default. I do see the poor
initial placement of proline hydrogens, but that's because the charmm
internal coordinates for them in the topology file are less than ideal.
Could you please send me the pdb where you see this hydrogen
deletion/readdition behavior?
Thanks,
Peter
moman_at_titus.u-strasbg.fr wrote:
> Thanks a lot to Mark, JC and Pedro for given me the right (and expected)
> anwser.
>
> Pedro: I have gone once more (quickily, I must confess) throgh the NAMD
> tutorial (namely the las chapter as you suggested), but I could not find
> an explicit anwser to my (obvious) question:
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/
>
> Surely it is somewhere there, but sitll I can no find it. Never mind.
> Thanks a million.
>
> Thaks to Peter as well for always being so regardful and helpful. However,
> you got everything this time wrong (mea culpa!). This was not a troll. I
> just allowed myself to use a little bit of irony (about last week's
> friendly controversy) WHILE asking a honest question AND making you note
> what it might be a little bug in the VDM autopsfgen (remarkable) feature:
> it seems it systematically asigns wrong coordinates to proline hydrogens
> (it removes them from the original file and add them again). I tried a
> couple of different protein files generated/converted with either
> OpenBabel, SPDBV and MOE and got similar results (wrong geometries) for
> the prolines.
>
> This only shows the point that I wanted to highlight with my irony: we are
> all (kind of) human ;-) and we are all in the same boat, aren't we?
>
> Cheers,
>
> Miro
>
>
>
>> Also... while I did get a chuckle out of the rest of your message, I
>> would recommend not feeding the troll. Even he would agree that it is
>> better for you to come with what you know and an open mind, than to be
>> unduly self deprecating.
>> Peter
>>
>> Edelmiro Moman wrote:
>>
>>> Hello,
>>>
>>> I do not know a work of Tcl scripting (or almost any other scripting
>>> language). In consequence, when I try to use a modified version of the
>>> NAMD sample.conf file, I get all kind of warning messages (if I use
>>> constraints, they tell me about bad geometries; otherwise they
>>> complain about high velocities) and the simulation is immediately
>>> aborted. I (ignorant) suspect that NAMD is starting directly with the
>>> MD simulation without doing a previous minimization (as I would wish).
>>> This is the relevant (I guess) fragment of the file:
>>> ______________________________________________________________
>>>
>>> #############################################################
>>> ## EXECUTION SCRIPT ##
>>> #############################################################
>>>
>>> # Minimization
>>> if {0} {
>>> minimize 100
>>> reinitvels $temperature
>>> }
>>>
>>> run 50000 ;# 100ps
>>> ______________________________________________________________
>>>
>>> First silly question: Am I right (by chance)?
>>>
>>> Second silly question: What can I do?
>>>
>>> Some clues: If the system has been previously minimized the simulation
>>> uses to runs uneventfully; but (!) Autopsfgen removes the hydrogens
>>> from my system and add them again, as a result of which the geometry
>>> of the prolines uses to be completely wrong and that takes me to the
>>> original problem.
>>>
>>> Kind regards,
>>>
>>> Miro
>>>
>>> P.S.: I am not as lazy as I am ignorant. However, as I am aware that
>>> my messages can hurt certain sensibilities, I have include a warning
>>> in the subject so that sensitive people do not have to read them.
>>> About unnecessarily increasing network traffic, I am very sorry about
>>> that and I plan to punish myself as soon as I can think of a suitable
>>> way of doing it.
>>>
>>>
>>>
>
>
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