AMBER Archive (2004)

Subject: AMBER: Close contact warnings

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue Feb 17 2004 - 08:29:57 CST

Dear all,

After I load amber prep file into xleap, I used check unit and was given the
following message:

Unit Editor: > check 4SN
Unit Editor: Checking '4SN'....
Unit Editor: WARNING: The unperturbed charge of the unit: -1.002000 is not zero.
Unit Editor: Warning: Close contact of 1.951802 angstroms between .R<4SN
1>.A<OS1 1> and .R<4SN 1>.A<C29 33>
Unit Editor: Warning: Close contact of 1.028610 angstroms between .R<4SN
1>.A<OS1 1> and .R<4SN 1>.A<H48 34>
Unit Editor: Warning: Close contact of 2.180533 angstroms between .R<4SN
1>.A<OS1 1> and .R<4SN 1>.A<O34 35>
Unit Editor: Warning: Close contact of 0.333375 angstroms between .R<4SN
1>.A<OS2 3> and .R<4SN 1>.A<H4 31>
Unit Editor: Warning: Close contact of 2.070560 angstroms between .R<4SN
1>.A<H62 9> and .R<4SN 1>.A<H49 47>
Unit Editor: Warning: Close contact of 1.621401 angstroms between .R<4SN
1>.A<ON3 25> and .R<4SN 1>.A<O50 28>
Unit Editor: Warning: Close contact of 0.323280 angstroms between .R<4SN
1>.A<ON3 25> and .R<4SN 1>.A<H51 29>
Unit Editor: Checking parameters for unit '4SN'.
Unit Editor: Checking for bond parameters.
Unit Editor: Checking for angle parameters.
Unit Editor: check: Warnings: 8
Unit Editor: Unit is OK.

I know they are just some warnings and I can save my prmtop and
inpcrd files without problems. But I suspect the Close Contact warnings are the
reason which make the subsequent minimizaion clash with the following abnormal
errors:

 Frac coord min, max: -116.333726 117.209705
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

I have run some short minimizaiton and got the output files every step. And I
found that the problems seem to be the VDWAALS = 26975175.0840 EEL =
-356.7031. Please anybody can give me some suggestion? Thanks a lot in advance.

Lan
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