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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Received on Thu Jun 07 2012 - 23:00:03 PDT
