Visualize your structure -- does it look distorted? If it does not look
distorted and it just appears that some atoms are too close, minimize the
structure (probably using more steepest decent steps than normal via the
"ncyc" input variable).
Tutorials and the manual both describe how to do this.
HTH,
Jason
On Fri, Jun 8, 2012 at 1:49 AM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> With checkoverlap I get the following output:
>
> OVERLAP: atoms 662 ( :43.HB2 ) and 4576 ( :289.42HC) are too close (
> 0.382)!
> OVERLAP: atoms 666 ( :43.OD2 ) and 4541 ( :289.C ) are too close (
> 0.639)!
> OVERLAP: atoms 666 ( :43.OD2 ) and 4542 ( :289.9HC ) are too close (
> 0.504)!
> OVERLAP: atoms 695 ( :46.HA ) and 4537 ( :289.6HC ) are too close (
> 0.504)!
> OVERLAP: atoms 752 ( :51.C ) and 4548 ( :289.12HC) are too close (
> 0.752)!
> OVERLAP: atoms 758 ( :52.CB ) and 4589 ( :289.28HC) are too close (
> 0.723)!
> OVERLAP: atoms 759 ( :52.HB1 ) and 4589 ( :289.28HC) are too close (
> 0.393)!
> OVERLAP: atoms 949 ( :63.HG12) and 4562 ( :289.21HC) are too close (
> 0.281)!
> OVERLAP: atoms 953 ( :63.HG22) and 4563 ( :289.C ) are too close (
> 0.645)!
> OVERLAP: atoms 1651 ( :110.CE1 ) and 4584 ( :289.24HC) are too close (
> 0.735)!
> OVERLAP: atoms 1655 ( :110.HH ) and 4532 ( :289.3HC ) are too close (
> 0.870)!
> OVERLAP: atoms 1673 ( :112.H ) and 4545 ( :289.11HC) are too close (
> 0.792)!
> OVERLAP: atoms 1676 ( :112.CB ) and 4544 ( :289.10HC) are too close (
> 0.798)!
> OVERLAP: atoms 1678 ( :112.CG2 ) and 4529 ( :289.C ) are too close (
> 0.863)!
> OVERLAP: atoms 1679 ( :112.HG21) and 4529 ( :289.C ) are too close (
> 0.527)!
> OVERLAP: atoms 1679 ( :112.HG21) and 4530 ( :289.HC ) are too close (
> 0.783)!
> OVERLAP: atoms 1684 ( :112.HG13) and 4593 ( :289.31HC) are too close (
> 0.794)!
> OVERLAP: atoms 1690 ( :112.O ) and 4570 ( :289.C ) are too close (
> 0.835)!
> OVERLAP: atoms 4525 ( :289.1HC ) and 4526 ( :289.2HC ) are too close (
> 0.557)!
> OVERLAP: atoms 4558 ( :289.18HC) and 4559 ( :289.19HC) are too close (
> 0.194)!
>
> What should I do to rectify the structure?
>
> On Fri, Jun 8, 2012 at 10:20 AM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
> > Can you help me what is the format of checkoverlap command? I just have
> > prmtop, inpcrd and pdb files. How to use this command with these files?
> >
> > Thanks
> >
> >
> > On Thu, Jun 7, 2012 at 4:49 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Thu, Jun 07, 2012, Asma Abro 28-FBAS/MSBI/F09 wrote:
> >> >
> >> > I am having trouble in minimization. It seems it got stuck at a point,
> >> no
> >> > error messages but its not moving further. Any suggestions?
> >> >
> >> > NSTEP ENERGY RMS GMAX NAME
> >> NUMBER
> >> > 1 NaN NaN 5.8908E+01 O
> 23176
> >> >
> >> > BOND = 446645.5044 ANGLE = 1672.6266 DIHED =
> >> 3358.8277
> >> > VDWAALS = ************* EEL = -73662.8982 EGB = NaN
> >> > 1-4 VDW = 999.3677 1-4 EEL = 11112.3672 RESTRAINT =
> 0.0000
> >>
> >> You input structure is bad, and probably has two atoms on top of each
> >> other.
> >> Use the "checkoverlap" command in ptraj to search for bad contacts.
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 08 2012 - 04:30:04 PDT
