Thank you Dr. Simmerling. I am trying to simulate a protein-DNA complex from a guessed unbound state to the known bound state. From X-ray experiment the essential part of the protein does not change much after forming complex with DNA so I add positional restraints to this part. The distang restraints were added to the DNA to maintain its featured structure. These restraints seem to work friendly during my implicit solvent tests.
Do you think I should remove them for explicit solvent simulation? Some of my results showed the protein and DNA can well maintain their structures in this situation.
Thanks again,
Shaowen
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling
Sent: Tuesday, April 21, 2009 2:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] help- regarding - TMD
yes since it is highly possible for these to conflict, you can't
restrain to a certain position in space and at the same time restrain
to RMSD of a reference. in principle it could be done if the user
understood waht they wanted, but in practice both the targeted md and
the cartesian restraints both use reference coordinates and currently
only 1 file is used. with all of the limitations it was more
straightforward to use one or the other but not both.
it's really hard to give more detail without having a general idea of
what you are trying to do with these multiple restraints, if you need
more help maybe you could just describe the goal of each of the
restraints in a few sentences.
On Mon, Apr 20, 2009 at 12:21 PM, Hu, Shaowen (JSC-SK)[Universities
Space Research Association USRA]. <shaowen.hu-1.nasa.gov> wrote:
> Thanks.
>
> According to the manual, once Cartesian positional restraints are applied, only rmsmask can be used. Is this right?
>
> I tested with a fitmask, but the input file cannot process.
>
> Thanks again,
> Shaowen
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling
> Sent: Monday, April 20, 2009 10:31 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] help- regarding - TMD
>
> check every restraint by calculating the values from the trajectory
> and make sure it does what you expected.
> also keep in mind that since you only specified an rmsmask, it will be
> the rms of that region alone and the calculation does not consider the
> reationship to other regions. a fitmask and rmsmask will make the rmsd
> have that value when overlapped to the fitmask atoms.
>
>
> On Mon, Apr 20, 2009 at 11:28 AM, Hu, Shaowen (JSC-SK)[Universities
> Space Research Association USRA]. <shaowen.hu-1.nasa.gov> wrote:
>> Dear Dr. Simmerling,
>>
>> Thanks for your comments. I have done some tests with implicit solvent. All results seem to be reasonable. The explicit solvent calculation also looks OK.
>>
>> Could you please list some ways to check the behavior of these restraints?
>>
>> Thanks a lot,
>> Shaowen
>>
>>
>> -----Original Message-----
>> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Carlos Simmerling
>> Sent: Monday, April 20, 2009 10:13 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] help- regarding - TMD
>>
>> I would be very careful with this setup to make sure everything is ok.
>> you have combined Cartesian positional restraints, NMR restraints (not
>> sure what they are since it is your disang file), and tgtmd
>> restraints.
>> you should check the behavior of each of these in your data.
>> they can in principle work together, but it is not obvious how to
>> design the restraints to work together, the code may not have been
>> well tested for the combination, and there is also possibility for
>> restraint conflicts.
>>
>> On Mon, Apr 20, 2009 at 11:05 AM, Hu, Shaowen (JSC-SK)[Universities
>> Space Research Association USRA]. <shaowen.hu-1.nasa.gov> wrote:
>>> Hi balaji,
>>>
>>> I just got some results for my system with explicit water. Here is my input file:
>>>
>>> &cntrl
>>> imin = 0, ntx = 1, nstlim = 1000000,
>>> dt = 0.001, ntc = 2, ntf = 2, tol = 0.000001,
>>> tempi = 300.0, temp0 = 300.0,
>>> scee = 1.2, cut = 9.0,
>>> ntpr = 50, ntwx = 500, ntwr = 500,
>>> ntt = 3, gamma_ln = 1.0,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 2.0,
>>> nscm = 0, nmropt = 1, ntr = 1,
>>> restraint_wt=1.0,
>>> restraintmask=':67-251,259-467.CA,C,N',
>>> itgtmd = 1, tgtrmsd = 66.8998, tgtmdfrc = 0.1,
>>> tgtrmsmask=":1-28",
>>> /
>>> &wt
>>> TYPE='TGTRMSD', istep1=1, istep2=1000000,
>>> value1 = 66.8998, value2 = 0.0,
>>> /
>>> &wt
>>> type="END",
>>> /
>>> LISTOUT=POUT
>>> DISANG=../../../14d.rst
>>>
>>> I used a restraint file for my ligand, which may not needed for you.
>>>
>>> I am doing test. Hope somebody having experience can give some comments.
>>>
>>> All the best,
>>> Shaowen
>>> ________________________________________
>>> From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu.hotmail.com]
>>> Sent: Wednesday, April 15, 2009 10:19 AM
>>> To: amber forumnew
>>> Subject: [AMBER] help- regarding - TMD
>>>
>>> Dear Amber ,
>>>
>>> I am giving targeted molecular dynamics with explicit water
>>>
>>> when i gave the following script
>>> sander.MPI is running .
>>> but when i see the out put file
>>> tail -f tmdscript.out
>>> its not printing any thing
>>> I could not find our the error
>>>
>>> help me out to solve this
>>>
>>> the script as below
>>> &cntrl
>>> imin = 0,
>>> irest = 0 ,
>>> ntb = 2,
>>> ntxo = 1,
>>> ntx =1,
>>> tempi =300.0,
>>> ntc=2,
>>> ntr =0,
>>> ntf = 2,
>>> nscm = 100,
>>> ntwr = 100
>>> ntpr = 100,
>>> ntwx = 100,
>>> ntwv =100,
>>> ntwe = 100,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> temp0 = 300.0
>>> nstlim = 2000000,
>>> dt = 0.002,
>>> cut = 10.0,
>>> itgtmd=1,
>>> tgtrmsd =0 ,
>>> tgtmdfrc =0.01,
>>> tgtfitmask= ":1- 76"
>>> tgtrmsmask= ":1- 76"
>>>
>>>
>>>
>>>
>>>
>>> /
>>> regards
>>> balaji
>>> UOM
>>>
>>>
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Received on Wed May 20 2009 - 12:09:33 PDT
