Hello,
Try visualizing your trajectory. I'm guessing this may be an imaging
artifact -- do you see the ligand and receptor flying away from one another
during the trajectory? If your complex is unbound, then Amber sees your
complex as separate molecules and images them separately (which may cause
the ligand to apparently fly away from the receptor). If you centered the
whole complex (receptor + ligand) and reimage around those, that will not
necessarily image your ligand back into place with your receptor.
This is how I suggest handling centering and imaging for non-covalently
bound complexes. For the sake of the example, let's assume that the
"receptor" is composed of residues 1-100, the first ligand is residue
101-110, and the second ligand is just residue 111.
To make sure that the complex is imaged properly (without regard to the
solvent), do the following:
center :1-100 mass origin
image origin center familiar **familiar is used for truncated octahedral
boxes**
If you want to make sure that the solvent is imaged around the complex, with
the complex at the center, do the above first, but afterward add the
following:
center :1-111 mass origin
image origin center familiar **familiar is used for truncated octahedral
boxes**
This should do it.
Hope this helps,
Jason
On Tue, Jan 11, 2011 at 11:22 AM, xueqin pang <pangxueqintea.yahoo.com.cn>wrote:
> Hello everyone,
>
> I am using Amber11 for MD
> simulation. It works nice but when run a segment for 20ns ( that is 5000
> snapshots) at a time, I got problem with the last several snapshots in the
> output dcd file. Taking the rmsd of the protein backbone for example it is
> about 230A while the normal ones are around 3A.
>
> I use ptraj
> from amber11 for rmsd calculation and it works well with other snapshots
> except with the ones form 40280-40460 ps and 60280-60460 ps that are
> the final 70 snapshots of npt13.dcd and npt14.dcd both the input and
> output are attached behind.
>
> By the way, the output energy temperature density pressure and volume are
> fine ...
>
> So what can we do to further finger out the problem and please let me know
> if you need other information to help
>
> Thanks very much
>
> input;
> trajin ../pro-lig-mw-Na6-Cl73-nve-npt8.binpos 1 230
> 2
> trajin ../pro-lig-mw-Na6-Cl73-npt9.dcd.gz 1 500
> 1
> trajin ../pro-lig-mw-Na6-Cl73-npt11.dcd.gz 1 2000
> 1
> trajin ../lig-pro-npt12.dcd.gz 1
> 2500 1
> trajin ../lig-pro-npt13.dcd 1
> 5000 1
> trajin ../lig-pro-npt14.dcd 1
> 5000 1
>
> center :1-204 mass origin
> image origin center familiar
> (also tried
> center .CA mass origin
> image origin center
> but no luck)
>
> rms first out pro-lig-bb.rms :1-204.CA,C,N
> time 4.0
> rms first out
> pro-lig-all.rms :1-204 time 4.0
>
> rms first out trp-a.rms
> :102 time 4.0
> rms first out trp-c.rms
> :204 time 4.0
>
> rms first out pro-lig-ABC-bb.rms :9-24,28-35,38-56.CA,C,N
> time 4.0
> rms first out pro-lig-ABC-all.rms
> :9-24,28-35,38-56 time 4.0
>
> rms first out pro-lig-A2B2C2-bb.rms :111-126,130-137,140-158.CA,C,N
> time
> 4.0
> rms first out pro-lig-A2B2C2-all.rms
> :111-126,130-137,140-158 time 4.0
>
> rms first out pro-lig-DE-bb.rms :61-68,72-85.CA,C,N
> time 4.0
> rms first out pro-lig-DE-all.rms
> :61-68,72-85 time 4.0
>
> rms first out pro-lig-D2E2-bb.rms
> :163-170,174-187.CA,C,N time 4.0
> rms first out pro-lig-D2E2-all.rms
> :163-170,174-187 time 4.0
>
> rms
> first out pro-lig-ABCA2B2C2-bb.rms
> :9-24,28-35,38-56,111-126,130-137,140-158.CA,C,N time
> 4.0
> rms first out pro-lig-ABCA2B2C2-all.rms
> :9-24,28-35,38-56,111-126,130-137,140-158 time 4.0
>
> rms first out pro-lig-DED2E2-bb.rms
> :61-68,72-85,163-170,174-187.CA,C,N time 4.0
> rms first out pro-lig-DED2E2.rms
> :61-68,72-85,163-170,174-187 time 4.0
>
>
>
> the output is like this:
> 40196.00 3.62379
> 40200.00 3.57787
> 40204.00
> 3.59396
> 40208.00 3.55176
> 40212.00 3.55755
> 40216.00 3.61072
> 40220.00 3.51690
> 40224.00 3.54457
> 40228.00 3.50856
> 40232.00 3.56595
> 40236.00 3.53495
> 40240.00 3.58373
> 40244.00 3.56591
> 40248.00 3.55274
> 40252.00 3.56384
> 40256.00 3.53552
> 40260.00 3.48354
> 40264.00 3.51672
> 40268.00 3.51680
> 40272.00 3.53946
> 40276.00 3.57942
> 40280.00 503.47216
> 40284.00 494.06059
> 40288.00 495.91581
> 40292.00 500.73311
> 40296.00 499.34041
> 40300.00 500.75827
> 40304.00 501.74491
> 40308.00 496.50253
> 40312.00 495.08027
> 40316.00
> 505.68574
> 40320.00 494.19087
> 40324.00 498.10471
> 40328.00 503.00141
> 40332.00 497.00654
> 40336.00 501.32159
> 40340.00 496.44208
> 40344.00 495.67839
> 40348.00 494.64808
> 40352.00 504.41720
> 40356.00 498.79969
> 40360.00 501.37176
> 40364.00 502.52509
> 40368.00 493.50986
> 40372.00 509.02993
> 40376.00 496.07358
> 40380.00 493.26818
> 40384.00 514.88252
> 40388.00 499.15561
> 40392.00 500.30938
> 40396.00 495.32700
> 40400.00 499.57580
> 40404.00 491.11505
> 40408.00 496.33841
> 40412.00 501.97969
> 40416.00 500.34191
> 40420.00 496.52573
> 40424.00 504.95763
> 40428.00 503.96328
> 40432.00 500.79367
> 40436.00 499.56972
> 40440.00 497.96784
> 40444.00 500.37400
> 40448.00 502.83966
> 40452.00
> 490.74727
> 40456.00 490.13810
> 40460.00 501.93728
> 40464.00 3.43600
> 40468.00 3.40314
> 40472.00 3.42939
> 40476.00 3.47919
> 40480.00 3.45434
> 40484.00 3.47105
> 40488.00 3.40627
> 40492.00 3.41956
> 40496.00 3.37335
> 40500.00 3.39285
> 40504.00 3.43147
> 40508.00 3.40280
> 40512.00 3.38379
> .
> .
> .
> .
> 60208.00 3.49698
> 60212.00 3.49558
> 60216.00 3.40186
> 60220.00 3.37891
> 60224.00 3.31956
> 60228.00 3.33794
> 60232.00 3.40359
> 60236.00 3.38580
> 60240.00 3.37928
> 60244.00
> 3.33913
> 60248.00 3.39330
> 60252.00 3.32382
> 60256.00 3.33229
> 60260.00 3.37229
> 60264.00 3.39414
> 60268.00 3.43121
> 60272.00 3.50082
> 60276.00 3.48373
> 60280.00 495.36233
> 60284.00 490.47826
> 60288.00 502.35940
> 60292.00 496.09247
> 60296.00 497.86649
> 60300.00 502.86591
> 60304.00 504.75363
> 60308.00 499.00816
> 60312.00 494.89123
> 60316.00 491.34819
> 60320.00 498.31413
> 60324.00 488.01539
> 60328.00 492.81843
> 60332.00 503.94241
> 60336.00 499.65280
> 60340.00 495.46360
> 60344.00 493.57554
> 60348.00 498.60472
> 60352.00 510.43223
> 60356.00 496.53787
> 60360.00 498.32477
> 60364.00 484.86662
> 60368.00
> 495.70181
> 60372.00 502.42476
> 60376.00 497.43111
> 60380.00 501.62143
> 60384.00 497.66322
> 60388.00 494.27478
> 60392.00 495.69731
> 60396.00 502.94928
> 60400.00 497.97454
> 60404.00 499.91530
> 60408.00 506.37999
> 60412.00 495.24463
> 60316.00 491.34819
> 60320.00 498.31413
> 60324.00 488.01539
> 60328.00 492.81843
> 60332.00 503.94241
> 60336.00 499.65280
> 60340.00 495.46360
> 60344.00 493.57554
> 60348.00 498.60472
> 60352.00 510.43223
> 60356.00 496.53787
> 60360.00 498.32477
> 60364.00 484.86662
> 60368.00 495.70181
> 60372.00 502.42476
> 60376.00 497.43111
> 60380.00 501.62143
> 60384.00 497.66322
> 60388.00 494.27478
> 60392.00 495.69731
> 60396.00 502.94928
> 60400.00 497.97454
> 60404.00
> 499.91530
> 60408.00 506.37999
> 60412.00 495.24463
> 60416.00 505.38098
> 60420.00 512.19207
> 60424.00 495.53304
> 60428.00 497.23037
> 60432.00 490.11806
> 60436.00 491.99509
> 60440.00 502.54092
> 60444.00 499.06300
> 60448.00 503.49534
> 60452.00 502.92540
> 60456.00 504.16717
> 60460.00 500.31077
>
>
>
> --- 11年1月10日，周一, xueqin pang <pangxueqintea.yahoo.com.cn> 写道：
>
> 发件人: xueqin pang <pangxueqintea.yahoo.com.cn>
> 主题: Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a
> time
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2011年1月10日,周一,下午11:08
>
>
>
>
> --- 11年1月10日，周一, case <case.biomaps.rutgers.edu> 写道：
>
> 发件人: case <case.biomaps.rutgers.edu>
> 主题: Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a
> time
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2011年1月10日,周一,下午10:05
>
> On Mon, Jan 10, 2011, xueqin pang wrote:
> >
> > I am using Amber11 for MD
> simulation. It works nice but when
> > run a segment for 20ns ( that is 5000 snapshots) at a time, I got
> > problem with the last several snapshots in the output dcd file. Taking
> > the rmsd of the protein backbone for example it is about 230A while
>
> You need to say exactly how you computed the rmsd. This is probably a
> simple
> matter of making sure you are correctly reading the box information from
> the
> trajectory file, but without even know what program you are using (much
> less
> what input) we can't help much.
>
> ...dac
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 11 2011 - 09:00:03 PST
