AMBER Archive (2009)

Subject: Re: [AMBER] help- regarding - TMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Apr 21 2009 - 18:35:42 CDT

do you mean the rmsd is for the protein-dna complex?
you could do it that way, but it's not at all clear if that's the way
the binding process works. you would need to do a lot of work to
validate it since you are making a lot of assumptions. codewise it
should work.

On Tue, Apr 21, 2009 at 6:40 PM, Hu, Shaowen (JSC-SK)[Universities
Space Research Association USRA]. <shaowen.hu-1_at_nasa.gov> wrote:
> The reference structure is a experimentally determined protein-DNA complex. I started by mannually taking the DNA a bit far away from the protein and then let the system reduce the rmsd of the DNA so that the DNA can return to the bound structure. I would like to see how some of the domains of the protein interact with DNA in this process. However, I am not sure whether this is an appropriate way. Please advice.
>
> Thanks a lot,
> Shaowen
>
> ________________________________________
> From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling_at_gmail.com]
> Sent: Tuesday, April 21, 2009 3:23 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] help- regarding - TMD
>
> just to be clear-
> positional (ntr=1) restraints on the protein
> distance restraints (nmropt=1) on the DNA
>
> what is the targeted MD for? what is the reference structure, and what
> is the rmsd that you are trying to change?
>
>
> On Tue, Apr 21, 2009 at 4:25 PM, Hu, Shaowen (JSC-SK)[Universities
> Space Research Association USRA]. <shaowen.hu-1_at_nasa.gov> wrote:
>> 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_at_ambermd.org [mailto:amber-bounces_at_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_at_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_at_ambermd.org [mailto:amber-bounces_at_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_at_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_at_ambermd.org [mailto:amber-bounces_at_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_at_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_at_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_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of balaji nagarajan [balaji_sethu_at_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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