AMBER Archive (2004)

Subject: AMBER: MM_PBSA calculation error

From: Jiten (jiten_at_postech.ac.kr)
Date: Thu Dec 30 2004 - 04:57:30 CST

Dear Amber user,

Using the same parameter set as given in the Examples of mm_pbsa modified for my requirements, I try to run the pbsa for stabilty calculation just for the first coordinate.

But it give the following massage

Use of uninitialized value in multiplication (*) at /theo1/tmp/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1368.
Use of uninitialized value in multiplication (*) at /theo1/tmp/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.

Therefore the output file do not contain the MS values.

MM
GB
PB
MS
1
 BOND = 956.1002 ANGLE = 2652.6422 DIHED = 3470.5582
 VDWAALS = -2741.5216 EEL = -21200.7246 EGB = -4266.6539
 1-4 VDW = 1223.5889 1-4 EEL = 13390.5651 RESTRAINT = 0.0000
corrected reaction field energy: -6997.966797

# MEAN STD
# =======================
ELE -7810.16 0.00
VDW -1517.93 0.00
INT 7079.30 0.00
GAS -2248.79 0.00
PBSUR 0.00 0.00
PBCAL -4171.68 0.00
PBSOL -4171.68 0.00
PBELE -11981.84 0.00
PBTOT -6420.48 0.00
GBSUR 0.00 0.00
GB -4266.65 0.00
GBSOL -4266.65 0.00
GBELE -12076.81 0.00
GBTOT -6515.45 0.00

But when I use the two crd files, I can see the MS values for the second coordinate.

I will highly appreciate if anybody can suggest me where to modify.

Thanking you in anticipation.

Sincerely,

N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19

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