AMBER Archive (2008)

Subject: Re: AMBER: restraintmask - reference file is not working

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Dec 18 2008 - 06:14:27 CST

Dirar,
after looking at your files, it seems that the region of atoms from your
rmsmask (2276-2299) is the same in both structures, that's why the rmsd is
zero. there is a region that differs, but it's at around atom # 3100, and
not 2276. also, when I did the align and rmsd (different selections, like
your sander input) in VMD I get 0 rmsd, not 8.87 like your earlier mail
said. maybe these aren't the right coordinates?
carlos

On Wed, Dec 17, 2008 at 2:51 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> maybe you can send me the inputs (inpcrd, prmtop, mdin and mdout) directly
> and I'll look at it and see what sander is doing.
> if it didn't read the refc it should not get an rmsd value, so I'm not sure
> what's wrong.
>
>
>
> On Wed, Dec 17, 2008 at 2:40 PM, Dirar Homouz <dirar_at_hotmail.com> wrote:
>
>> Hi Carlos,
>>
>> The rmsd that I get from sander output is:
>>
>> Current RMSD from reference: 0.094
>> Current target RMSD: 0.000
>>
>>
>>
>> The rmsd that I get from vmd is 8.87.
>>
>> It looks like the reference file is not read. Am I defining it in the
>> wrong way?
>>
>> -Dirar
>> ------------------------------
>> Date: Wed, 17 Dec 2008 08:19:25 -0500
>>
>> From: carlos.simmerling_at_gmail.com
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: restraintmask - reference file is not working
>>
>> sounds like it should be working. does the initial/final rms match what
>> you get in the viz program that you are using the view the trajectory?
>> I just don't have enough detail to make any more suggestions. you
>> definitely don't want to use ntr=1 with this.
>>
>>
>> On Wed, Dec 17, 2008 at 4:41 AM, Dirar Homouz <dirar_at_hotmail.com> wrote:
>>
>> I tried using the fit mask and rms mask. However, the results are the
>> same. To use the fit mask and rms mask, I used two different
>> control input files:
>>
>> The first one with the position restraints:
>>
>> &cntrl
>> imin = 0, ntb = 0,
>> igb = 0, ntpr = 1, ntwx = 1,
>> ntt = 3, gamma_ln = 1.0,
>> tempi = 300.0, temp0 = 300.0
>> nstlim = 100000, dt = 0.001,
>> cut = 12.0,
>> itgtmd= 1,
>> tgtmdfrc= 100.0,
>> ntr =1, ntrx=1, restraint_wt=10.0,
>> tgtrmsmask='@2276-2299',
>> restraintmask='@1-2299',
>> /
>>
>>
>> And the second one without:
>>
>>
>> &cntrl
>> imin = 0, ntb = 0,
>> igb = 0, ntpr = 1, ntwx = 1,
>> ntt = 3, gamma_ln = 1.0,
>> tempi = 300.0, temp0 = 300.0
>> nstlim = 100000, dt = 0.001,
>> cut = 12.0,
>> itgtmd= 1,
>> tgtmdfrc= 100.0,
>> ntr =0, ntrx=1,
>> tgtrmsmask='@2276-2299',
>> tgtfitmask='@1-2299',
>> /
>>
>>
>> In both cases the result is the same. RMS goes down, the restraint energy
>> is non-zero. However, the structure is still fluctuating about
>> the inpcrd coordinates.
>>
>> -Dirar
>>
>> ------------------------------
>> Date: Tue, 16 Dec 2008 20:05:03 -0500
>>
>> From: carlos.simmerling_at_gmail.com
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: restraintmask - reference file is not working
>>
>> then the mask is ok, but likely it's the best-fit is shifting the region
>> to fit the refc without needing to change the conformation. try using a fit
>> mask for the whole protein and rms mask just for that region.
>>
>> On Tue, Dec 16, 2008 at 7:51 PM, Dirar Homouz <dirar_at_hotmail.com> wrote:
>>
>> Hi Carlos again,
>>
>> I'm sorry. I sent the information from the wrong output file. For the
>> system i'm running the output file says:
>>
>> Mask @2276-2299; matches 24 atoms
>>
>> The restraint energy is non-zero.
>>
>> -Dirar
>>
>> ------------------------------
>> Date: Tue, 16 Dec 2008 19:38:14 -0500
>> From: carlos.simmerling_at_gmail.com
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: restraintmask - reference file is not working
>>
>> look in the sander output- does sander recognize the restraints? does it
>> list the correct # of atoms matching the mask? if so, is the restraint
>> energy non-zero?
>> are the atoms shifted as a group? meaning even if they are shifted, is it
>> possible that the best-fit process shifts them back to perfect alignment to
>> refc? if so, perhaps you want a separate fit mask and rms mask.
>> check these, it's the important information you need to know what's going
>> on.
>>
>>
>> On Tue, Dec 16, 2008 at 7:05 PM, Dirar Homouz <dirar_at_hotmail.com> wrote:
>>
>> Dear Amber users,
>>
>> I'm trying to pull a certain structure using restraintmask from an initial structure
>> defined by the input file "inpcrd" to a final structure defined by reference file
>> "refc".
>>
>>
>>
>> I'm using the following input file
>>
>> ************************************************************
>> &cntrl
>> imin = 0, ntb = 0,
>> igb = 0, ntpr = 100, ntwx = 100,
>> ntt = 3, gamma_ln = 1.0,
>>
>>
>>
>> tempi = 300.0, temp0 = 300.0
>> nstlim = 100000, dt = 0.001,
>> cut = 12.0
>> ntr=1,
>> ntrx=1,
>> restraint_wt=100.0,
>> restraintmask='@2276-2299',
>> /
>> ************************************************************
>>
>>
>>
>> with the following command
>>
>> $AMBERHOME/exe/sander -O -i pull.in -o pull.out -c inpcrd -p prmtop -r
>> rst -ref refc
>>
>> The inpcrd file is different from the refc file. The last 24 atoms are
>>
>>
>>
>> shifted from their initial positions.
>>
>> The code runs fine. However, it doesn't move the structure to the
>> coordinates defined by the refc file. I'm not sure why is the refc file
>> is not recognized?
>>
>>
>>
>>
>>
>> -Dirar
>>
>>
>>
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