Dear Dr. Simmerling
I have computed the RMSD value with Maestro.
The reference structure that i use is the activated conformation of the
protein .
My idea is to try to compute the trajectory from the inactive (X-ray
structure) to active conformation (X-ray structure) looking for the
most moving residues. Despite are two conformations of the same protein
one (active) is "larger" that the other, indeed the inactive was
solvatated with 46879 water molecules and the active one with 69302.
Thus, to have the same number of atoms i have stripped by parmed the
excess water molecules, does could it affect the water box integrity?
Following your suggestion i have tried with the inpcrd as the reference
structure and a smaller restraint energy and i have RMSD=0 and MD is
going on.
Thank you very much for your advises.
Best Regards
Antonio
On 12/22/2014 03:05 PM, Carlos Simmerling wrote:
> yes, the restraint energy is really high. can you give more info about the
> RMSD value? what exactly is the reference structure, and how did you
> calculate the RMSD outside Amber? Also, what happens if you use the inpcrd
> as the reference structure- do you get RMSD=0 and stable MD?
>
> On Mon, Dec 22, 2014 at 8:52 AM, antonio.coluccia.uniroma1.it <
> antonio.coluccia.uniroma1.it> wrote:
>> ce
>> Dear Dr. Simmerling
>> thanks for your reply.
>> I have already tested the MD without the tgtmd for both protein
>> conformations and it works fine.
>> I have also tried with just one CPU with smaller nstlim and ntpr=1 but i
>> have the same frozen state with the following output:
>>
>> 4. RESULTS
>>
>> --------------------------------------------------------------------------------
>>
>> | # of SOLUTE degrees of freedom (RNDFP): 454224.
>> | # of SOLVENT degrees of freedom (RNDFS): 0.
>> | NDFMIN = 454218. NUM_NOSHAKE = 0 CORRECTED RNDFP = 454218.
>> | TOTAL # of degrees of freedom (RNDF) = 454218.
>>
>> NSTEP = 0 TIME(PS) = 120.000 TEMP(K) = 0.00 PRESS
>> = 0.0
>> Etot = 4013136.4603 EKtot = 0.0000 EPtot =
>> 4013136.4603
>> BOND = 2060.5152 ANGLE = 5811.0946 DIHED = 7670.1463
>> 1-4 NB = 2481.8886 1-4 EEL = 22414.5833 VDWAALS =
>> 40379.6693
>> EELEC = -417775.1195 EGB = -131754.0231 RESTRAINT =
>> 4481847.7057
>> EAMBER (non-restraint) = -468711.2454
>> Current RMSD from reference: 18.248
>> Current target RMSD: 0.000
>>
>> My concern are about the Current RMSD from reference value it should be 2.
>>
>> thank you very much
>>
>> Antonio
>>
>>
>>
>> On 12/22/2014 02:42 PM, Carlos Simmerling wrote:
>>> if you haven't already done this, I suggest (1) making sure MD without
>> the
>>> tgtmd works fine using the same input coordinates and (2) try the tgtmd
>>> using sander with a single CPU and shorter nstlim, with ntpr=1 so you can
>>> get a better idea of whether something is wrong with the energies. also,
>>> what is your reference coordinate set?
>>>
>>> On Mon, Dec 22, 2014 at 8:31 AM, antonio.coluccia.uniroma1.it <
>>> antonio.coluccia.uniroma1.it> wrote:
>>>> Dear All,
>>>> I would like to carry out a target dynamics.
>>>> Following suggestion fro the mailing list
>>>> i have computed parameters for starting and reference conformations of
>>>> studied protein with leap,
>>>> checked the number of atoms and computed the minimization for both
>>>> conformations.
>>>> When i use sander to carry out target dynamics calculation the system
>>>> was frozen at the step 0 with the RMSD higher that the real one and with
>>>> CPU working at 100%.
>>>> I suppose that the problem could be the size of the water boxes for the
>>>> two protein conformations
>>>> but i do not know how to solve the problem
>>>> Do you have any suggestions?
>>>>
>>>> My input file is:
>>>> &cntrl
>>>> nstlim= 10000000, dt=0.002, temp0=300.0, ntt=1,
>>>> ntpr=500, ntwr=5000, ntwx=5000,
>>>> ntx=1, ntpr=100,
>>>> ntf=1, ntc=1, ntb=0,
>>>> igb=1, gbsa=0,
>>>> nsnb=25,
>>>> itgtmd=1, tgtmdfrc=10,
>>>> tgtfitmask=":1-674.CA,N,C,O",
>>>> tgtrmsmask=":1-674.CA,N,C,O",
>>>>
>>>> &end
>>>> &wt type='TGTRMSD', istep1=1, istep2=10000000, value1=2.00 , value2=0.0,
>>>> > &end
>>>>
>>>>
>>>> Any help will be really appreciated.
>>>>
>>>> with best regards
>>>>
>>>> Antonio
>>>>
>>>> --
>>>> Antonio Coluccia, Ph.D.
>>>> Department of Chemistry and Drugs Tecnology
>>>> La Sapienza University
>>>> Rome 00185
>>>> Piazzale Aldo Moro 5
>>>> antonio.coluccia.uniroma1.it
>>>> mobile: 00393406113351
>>>>
>>>>
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>> --
>> Antonio Coluccia, Ph.D.
>> Department of Chemistry and Drugs Tecnology
>> La Sapienza University
>> Rome 00185
>> Piazzale Aldo Moro 5
>> antonio.coluccia.uniroma1.it
>> mobile: 00393406113351
>>
>>
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>>
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--
Antonio Coluccia, Ph.D.
Department of Chemistry and Drugs Tecnology
La Sapienza University
Rome 00185
Piazzale Aldo Moro 5
antonio.coluccia.uniroma1.it
mobile: 00393406113351
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Received on Mon Dec 22 2014 - 07:00:03 PST
