Hi Carlos,
I read the publication in which you are using partial REMD, but I was
not able to find any hint on how to set up the input files as well as
the system.
Would you be so kind and give me some straightforward hints? I'm
considering this as an alternative to the NEB approach because of some
problems in the setting up of the system (however I'm still trying).
Further, concerning my previous email aboout NEB, I'm currently working
with a larger system (about 660 residues) and I am experiencing some
problems when using addles in order to prepare the starting NEB.prmtop
and NEB.inpcrd. I get rid of the SIZE.h problem by increasing the atom,
bond and angle parameters but when I repeat the addles run I get a
strange error (not reported in the amber mailing list so far. And here
it comes:
Amber11 Module: addles
set up Locally Enhanced Sampling topology
add_les> file rprm name=(3h77-1.prmtop) read
The following unit number was assigned 26
| New format PARM file being parsed.
| Version = 1.000 Date = 04/15/11 Time = 17:35:52
Checking topology sizes against compiled limits
Checking topology sizes against compiled limits
add_les> file rcrd name=(3h77-1.inpcrd) pack=2 read
The following unit number was assigned 27
urcrd: 27
Coordinates only from unit 27
Reading coordinates from input file
Reading coordinates from input file
add_les> file wprm name=(neb.prmtop) wovr
The following unit number was assigned 28
add_les> file wcrd name=(neb.inpcrd) wovr
The following unit number was assigned 29
add_les> action
add_les> # use original mass
*_Problem in line read..._*
And then the addless.out file stops without agiving any output.
Any suggestion on which screw I can work on to solve this?
Many thanks for your kindness,
best regards
Matthias Negri
> Hi Matthias,
> you are free to set these as you wish, just as you suggest. You might
> fix part of the protein in space, and map the path for another set of
> atoms moving relative to the first.
> we'll work on getting more tutorials for these, but as always finding
> time to write tutorials can be a challenge.
> carlos
>
> On Tue, Apr 12, 2011 at 9:31 AM, Matthias Negri
> <m.negri.mx.uni-saarland.de> wrote:
>> Hi,
>> first of all, this subject is very interesting for us and it might be of
>> general interest (perhaps) to get a broader tutorial, not only focusing
>> on small molecules.
>>
>> Then, here comes my question:
>> I read through the journal referenced as well as the tutorial, but I
>> still have some doubts concerning the usage of tgtfitmask and tgtrmsmask
>> in NEB. As far I have understood in multiple MD these can be different,
>> which might be helpfull when only parts of the proteins are going to be
>> considered. To bring a direct example, I'd tried
>> tgtfitmask=":1-207,214-536,543-658.CA,N,C,O,H,HA" (the protein part
>> which should not move) and tgtrmsmask=":208-213.CA,N,C,O" (the changing
>> part of the protein, expected to move along according to the given RMS
>> value) to simulate the progression from state A to state B.
>> Might I also apply this criteria to NEB or do I need to choose the same
>> range of residues, eventually using different atom types (on which to
>> apply the NEB force, as in the NEB tutorial)?
>>
>> Best regards,
>>
>> Matthias
>>> the NEB option in sander is probably the best Amber option for this.
>>> You could also run targeted MD, starting with one structure and using
>>> the RMSD restraint to force it to the other, but that can give high
>>> forces at the start and tends to give direct paths that may not be
>>> optimal.
>>>
>>> If you go with NEB, use the Amber11 version. A tutorial and journal
>>> reference for our NEB version can be found at
>>> http://ambermd.org/tutorials/advanced/tutorial5_amber11/
>>>
>>>
>>> On Tue, Apr 12, 2011 at 7:43 AM, Bernhard Poll
>>> <poll.chemie.uni-hamburg.de> wrote:
>>>> Hi Amber users,
>>>>
>>>>
>>>>
>>>> I've got some questition about MD's. Is it possible to define some start and
>>>> end structure (and may be a transition state) of a protein in Amber and run
>>>> a MD simulation? We know these points from crystal analysis and we're just
>>>> wondering if it is possible to run the transition so we can understand this
>>>> behavior.
>>>>
>>>>
>>>>
>>>> Thanks in advance
>>>>
>>>>
>>>>
>>>> Bernhard
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 21 2011 - 07:30:03 PDT
