AMBER Archive (2009)

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

From: Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (shaowen.hu-1_at_nasa.gov)
Date: Tue Apr 21 2009 - 17:40:36 CDT

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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