AMBER: rdparm problem

From: Lijiang Yang <lijiangy.uci.edu>
Date: Mon, 9 Aug 2004 15:43:10 -0700

Hi All,
  It seems that rdparm in Amber8 doesn't recognize perturbed parm files in
the new format: perturbed bonds and angles information read by rdparm
are not correct. However if I transform the new format into the old
format, rdparm can give correct parameters on both perturbed bonds and
angles. Is this a known problem?

Another issue is that every time when perturbed dihedrals are read, the
program terminates (segmentation fault, core dumped). This happens in
both old and new formats.

My workstation is Intel P4 with Fedora Core 1. It seems that amber8
install is not a problem since all tests are passed. Followings are
outputs from rdparm. I have attached the parm files in both new and old
formats.

Thanks a lot for your help!

1. Rdparm output of New Format prmtop file: (wrong)

RDPARM MENU: pertbonds :1
Mask [:1] represents 14 atoms

Bond
lambda Kb Req atom names (numbers)
0 1: 0.00 0.000 :1.CB :1.CB (1,1)
1 1: 0.00 0.000 :1.CB :1.CB (1,1)

0 2: 0.00 0.000 :1.CB :1.CB (1,1)
1 2: 0.00 0.000 :1.CB :1.CB (1,1)

0 3: 0.00 0.000 :1.CB :1.CB (1,1)
1 3: 0.00 0.000 :1.CB :1.CB (1,1)

0 4: 0.00 0.000 :1.CB :1.CB (1,1)
1 4: 0.00 0.000 :1.CB :1.CB (1,1)

0 5: 0.00 0.000 :1.CB :1.CB (1,1)
1 5: 0.00 0.000 :1.CB :1.CB (1,1)

0 6: 0.00 0.000 :1.CB :1.CB (1,1)
1 6: 0.00 0.000 :1.CB :1.CB (1,1)

0 7: 0.00 0.000 :1.CB :1.CB (1,1)
1 7: 0.00 0.000 :1.CB :1.CB (1,1)

0 8: 0.00 0.000 :1.CB :1.CB (1,1)
1 8: 0.00 0.000 :1.CB :1.CB (1,1)

0 9: 0.00 0.000 :1.CB :1.CB (1,1)
1 9: 0.00 0.000 :1.CB :1.CB (1,1)

0 10: 0.00 0.000 :1.CB :1.CB (1,1)
1 10: 0.00 0.000 :1.CB :1.CB (1,1)

0 11: 0.00 0.000 :1.CB :1.CB (1,1)
1 11: 0.00 0.000 :1.CB :1.CB (1,1)

0 12: 0.00 0.000 :1.CB :1.CB (1,1)
1 12: 0.00 0.000 :1.CB :1.CB (1,1)

0 13: 0.00 0.000 :1.CB :1.CB (1,1)
1 13: 0.00 0.000 :1.CB :1.CB (1,1)


RDPARM MENU: pertangles :1
Mask [:1] represents 14 atoms

Angle
lambda Kthet Req atom names (numbers)
0 1: 50.000 109.50 :1.CB :1.HB2 :1.CB (1,2,1)
1 1: 50.000 109.50 :1.CB :1.HB2 :1.CB (1,2,1)

0 2: 50.000 109.50 :1.HB3 :1.CB :1.CG (3,1,4)
1 2: 50.000 109.50 :1.HB3 :1.CB :1.CG (3,1,4)

0 3: 40.000 109.50 :1.CB :1.HB1 :1.CG (1,14,4)
1 3: 50.000 109.50 :1.CB :1.HB1 :1.CG (1,14,4)

0 4: 50.000 109.50 :1.HG :1.CG :1.CD1 (5,4,6)
1 4: 50.000 109.50 :1.HG :1.CG :1.CD1 (5,4,6)

0 5: 50.000 109.50 :1.CG :1.CD2 :1.CD1 (4,10,6)
1 5: 50.000 109.50 :1.CG :1.CD2 :1.CD1 (4,10,6)

0 6: 40.000 109.50 :1.HD11 :1.CD1 :1.HD12 (7,6,8)
1 6: 50.000 109.50 :1.HD11 :1.CD1 :1.HD12 (7,6,8)

0 7: 40.000 109.50 :1.CD1 :1.HD13 :1.CD2 (6,9,10)
1 7: 50.000 109.50 :1.CD1 :1.HD13 :1.CD2 (6,9,10)

0 8: 50.000 109.50 :1.HD21 :1.CD2 :1.HD22 (11,10,12)
1 8: 50.000 109.50 :1.HD21 :1.CD2 :1.HD22 (11,10,12)

0 9: 50.000 109.50 :1.CD2 :1.HD23 :1.HD23 (10,13,13)
1 9: 50.000 109.50 :1.CD2 :1.HD23 :1.HD23 (10,13,13)

0 10: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 10: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 11: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 11: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 12: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 12: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 13: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 13: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 14: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 14: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 15: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 15: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 16: 40.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 16: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 17: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 17: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 18: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 18: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 19: 40.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 19: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 20: 40.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 20: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 21: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 21: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 22: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 22: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 23: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 23: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)

0 24: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)
1 24: 50.000 109.50 :1.HD23 :1.HD23 :1.HD23 (13,13,13)


RDPARM MENU: pertdihedrals :1
Mask [:1] represents 14 atoms

Dihedral pk phase pn atoms
0 1: 0.156 0.00 3.0 :1.CB :1.CG :1.HG :1.CB (1,4,5,1)
1 1:
11436558031142067792769009694484533572909034200973685803444585963360334650515
3745443263863833514369884869972173040310158088385970899400811909070808341232499308323032
1458742602676115692332550692199262578348939886493436218700686512716605319806976.000
0.00
0.0 :1.CB :1.CG :1.HG :1.CB (1,4,5,1)

0 2: 0.150 0.00 3.0 :1.CG :1.CD1 :1.CB :1.CG (4,6,1,4)
1 2: 0.160 0.00 3.0 :1.CG :1.CD1 :1.CB :1.CG (4,6,1,4)

Segmentation fault (core dumped)


2. Rdparm output for old format prmtop file:(correct)

RDPARM MENU: pertbonds :1
Mask [:1] represents 14 atoms

Bond
lambda Kb Req atom names (numbers)
0 1: 340.00 1.090 :1.CB :1.HB2 (1,2)
1 1: 340.00 1.090 :1.CB :1.HB2 (1,2)

0 2: 340.00 1.090 :1.CB :1.HB3 (1,3)
1 2: 340.00 1.090 :1.CB :1.HB3 (1,3)

0 3: 310.00 1.526 :1.CB :1.CG (1,4)
1 3: 310.00 1.526 :1.CB :1.CG (1,4)

0 4: 340.00 1.090 :1.CB :1.HB1 (1,14)
1 4: 340.00 1.090 :1.CB :1.HB1 (1,14)

0 5: 340.00 1.090 :1.CG :1.HG (4,5)
1 5: 340.00 1.090 :1.CG :1.HG (4,5)

0 6: 310.00 1.526 :1.CG :1.CD1 (4,6)
1 6: 310.00 1.526 :1.CG :1.CD1 (4,6)

0 7: 310.00 1.526 :1.CG :1.CD2 (4,10)
1 7: 310.00 1.526 :1.CG :1.CD2 (4,10)

0 8: 340.00 1.090 :1.CD1 :1.HD11 (6,7)
1 8: 340.00 1.090 :1.CD1 :1.HD11 (6,7)

0 9: 340.00 1.090 :1.CD1 :1.HD12 (6,8)
1 9: 340.00 1.090 :1.CD1 :1.HD12 (6,8)

0 10: 340.00 1.090 :1.CD1 :1.HD13 (6,9)
1 10: 340.00 1.090 :1.CD1 :1.HD13 (6,9)

0 11: 340.00 1.090 :1.CD2 :1.HD21 (10,11)
1 11: 340.00 1.090 :1.CD2 :1.HD21 (10,11)

0 12: 340.00 1.090 :1.CD2 :1.HD22 (10,12)
1 12: 340.00 1.090 :1.CD2 :1.HD22 (10,12)

0 13: 340.00 1.090 :1.CD2 :1.HD23 (10,13)
1 13: 340.00 1.090 :1.CD2 :1.HD23 (10,13)

RDPARM MENU: pertangles :1
Mask [:1] represents 14 atoms

Angle
lambda Kthet Req atom names (numbers)
0 1: 50.000 109.50 :1.CB :1.CG :1.HG (1,4,5)
1 1: 50.000 109.50 :1.CB :1.CG :1.HG (1,4,5)

0 2: 40.000 109.50 :1.CB :1.CG :1.CD1 (1,4,6)
1 2: 40.000 109.50 :1.CB :1.CG :1.CD1 (1,4,6)

0 3: 40.000 109.50 :1.CB :1.CG :1.CD2 (1,4,10)
1 3: 40.000 109.50 :1.CB :1.CG :1.CD2 (1,4,10)

0 4: 35.000 109.50 :1.HB2 :1.CB :1.HB3 (2,1,3)
1 4: 35.000 109.50 :1.HB2 :1.CB :1.HB3 (2,1,3)

0 5: 50.000 109.50 :1.HB2 :1.CB :1.CG (2,1,4)
1 5: 50.000 109.50 :1.HB2 :1.CB :1.CG (2,1,4)

0 6: 35.000 109.50 :1.HB2 :1.CB :1.HB1 (2,1,14)
1 6: 35.000 109.50 :1.HB2 :1.CB :1.HB1 (2,1,14)

0 7: 50.000 109.50 :1.HB3 :1.CB :1.CG (3,1,4)
1 7: 50.000 109.50 :1.HB3 :1.CB :1.CG (3,1,4)

0 8: 35.000 109.50 :1.HB3 :1.CB :1.HB1 (3,1,14)
1 8: 35.000 109.50 :1.HB3 :1.CB :1.HB1 (3,1,14)

0 9: 50.000 109.50 :1.CG :1.CB :1.HB1 (4,1,14)
1 9: 50.000 109.50 :1.CG :1.CB :1.HB1 (4,1,14)

0 10: 50.000 109.50 :1.CG :1.CD1 :1.HD11 (4,6,7)
1 10: 50.000 109.50 :1.CG :1.CD1 :1.HD11 (4,6,7)

0 11: 50.000 109.50 :1.CG :1.CD1 :1.HD12 (4,6,8)
1 11: 50.000 109.50 :1.CG :1.CD1 :1.HD12 (4,6,8)

0 12: 50.000 109.50 :1.CG :1.CD1 :1.HD13 (4,6,9)
1 12: 50.000 109.50 :1.CG :1.CD1 :1.HD13 (4,6,9)

0 13: 50.000 109.50 :1.CG :1.CD2 :1.HD21 (4,10,11)
1 13: 50.000 109.50 :1.CG :1.CD2 :1.HD21 (4,10,11)

0 14: 50.000 109.50 :1.CG :1.CD2 :1.HD22 (4,10,12)
1 14: 50.000 109.50 :1.CG :1.CD2 :1.HD22 (4,10,12)

0 15: 50.000 109.50 :1.CG :1.CD2 :1.HD23 (4,10,13)
1 15: 50.000 109.50 :1.CG :1.CD2 :1.HD23 (4,10,13)

0 16: 50.000 109.50 :1.HG :1.CG :1.CD1 (5,4,6)
1 16: 50.000 109.50 :1.HG :1.CG :1.CD1 (5,4,6)

0 17: 50.000 109.50 :1.HG :1.CG :1.CD2 (5,4,10)
1 17: 50.000 109.50 :1.HG :1.CG :1.CD2 (5,4,10)

0 18: 40.000 109.50 :1.CD1 :1.CG :1.CD2 (6,4,10)
1 18: 40.000 109.50 :1.CD1 :1.CG :1.CD2 (6,4,10)

0 19: 35.000 109.50 :1.HD11 :1.CD1 :1.HD12 (7,6,8)
1 19: 35.000 109.50 :1.HD11 :1.CD1 :1.HD12 (7,6,8)

0 20: 35.000 109.50 :1.HD11 :1.CD1 :1.HD13 (7,6,9)
1 20: 35.000 109.50 :1.HD11 :1.CD1 :1.HD13 (7,6,9)

0 21: 35.000 109.50 :1.HD12 :1.CD1 :1.HD13 (8,6,9)
1 21: 35.000 109.50 :1.HD12 :1.CD1 :1.HD13 (8,6,9)

0 22: 35.000 109.50 :1.HD21 :1.CD2 :1.HD22 (11,10,12)
1 22: 35.000 109.50 :1.HD21 :1.CD2 :1.HD22 (11,10,12)

0 23: 35.000 109.50 :1.HD21 :1.CD2 :1.HD23 (11,10,13)
1 23: 35.000 109.50 :1.HD21 :1.CD2 :1.HD23 (11,10,13)

0 24: 35.000 109.50 :1.HD22 :1.CD2 :1.HD23 (12,10,13)
1 24: 35.000 109.50 :1.HD22 :1.CD2 :1.HD23 (12,10,13)


RDPARM MENU: pertdihedrals :1
Mask [:1] represents 14 atoms

Dihedral pk phase pn atoms
0 1: 0.156 0.00 3.0 :1.CB :1.CG :1.CD1 :1.HD11 (1,4,6,7)
1 1: 0.160 0.00 3.0 :1.CB :1.CG :1.CD1 :1.HD11 (1,4,6,7)

0 2: 0.156 0.00 3.0 :1.CB :1.CG :1.CD1 :1.HD12 (1,4,6,8)
1 2: 0.160 0.00 3.0 :1.CB :1.CG :1.CD1 :1.HD12 (1,4,6,8)

Segmentation fault (core dumped)

---------------------------------------------------
Lijiang Yang, Ph.D.
Dr. Ray Luo's Group
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Lab: (949)824-9562
e-mail: lijiangy.uci.edu


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Received on Tue Aug 10 2004 - 00:53:00 PDT
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