AMBER Archive (2009)

Subject: [AMBER] Question about &dipoles printing in AMBER 8

From: Karen Callahan (
Date: Mon May 25 2009 - 18:46:00 CDT


I have been looking into printing dipoles using sander in AMBER8, (by this I do mean the normal version of sander and using polarizable force fields, not the one adapted by Martin Mucha).

I am using a box with 464 waters to do this. I would like to be able to individually print the dipole information for every water.

When I designate a different group for each of the waters, only 463 of the 464 groups have dipoles printed. This is independent of the order of the residues, I can put any residue 1-464 in any group, and it will be the 464th group missing.

When I designate fewer than 464 groups, all groups designated have their dipoles printed, regardless of which residue I put in which group. (so long as no residue or atom is part of two groups).

A caveat: If I have a mix of groups with one residue and a group containing more than one residue (though none repeated), whatever is the last group in the list (even if I have less than 464 groups) is not printed.

When I designate more than 464 groups, only dipoles of 463 are printed.

If a residue is part of more than one group, the earlier group selections containing it will give the center of mass as NaN and all the dipole information as O's. It seems that the atom or residue is only a member of the group farthest down in the list that it is named in.

It seems I can have one group include all the atoms or residues of the system if this is the only group selection. But I cannot check this really includes all the residues.

I am sure I have 464 waters. What am I doing wrong? Why can't I print the information for all 464 waters individually? Is there a reason I can't?

Karen Callahan
UC Irvine

I have been using variations of an input file in the form:
        imin = 0,

        ntx = 5, irest = 1,

        ntpr = 100, ntwr = 100, ntwx = 1000,
        ntwe = 100,
        ntxo = 1,
        iwrap = 0,

        ntf = 2, ntb = 1,
        cut = 10, ipol = 1,
        nstlim = 100000, dt = 0.001, t = 0,
        ntp = 0, pres0 = 1.0, comp = 44.6,
        ntt = 1, temp0 = 300.0, tautp = 1.0,

        ntc = 2, tol = 0.00001,

      use_pme=1, eedmeth=1, vdwmeth=0
      indmeth=1, diptol=0.0001
RES 461
RES 462
RES 463
RES 464


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