AMBER Archive (2008)

Subject: AMBER: Fwd: positive potential energy and large 1-4 EEL

From: Mey Khalili (ejdehayedosar_at_gmail.com)
Date: Fri Mar 07 2008 - 10:54:28 CST

  I have had problems subscribing to amber. My apologies for multiple
postings.....

---------- Forwarded message ----------
From: Mey Khalili <ejdehayedosar_at_gmail.com>
Date: Fri, Mar 7, 2008 at 11:31 AM
Subject: positive potential energy and large 1-4 EEL
To: amber_at_scripps.edu

 Dear amber,

   I am trying to make a modified Adenine nucleotide for RNA with amber9. I
followed the antechamber instructions. The charges came from Gaussian. The
structure looks like it should and after minimization and 1ns of MD, it
still looks OK. The problem is that its potential energy is positive. I
compared its partial charges and its internal energies against those of RA.
Charges look similar. This is the breakdown of the energies at the end of
minimization for both:

RA:
   NSTEP ENERGY RMS GMAX NAME NUMBER
   7299 -6.3915E+01 7.0464E-05 3.9110E-04 H62 21

 BOND = 0.8902 ANGLE = 5.4119 DIHED =
19.9286
 VDWAALS = -5.2890 EEL = -103.3183 HBOND =
0.0000
 1-4 VDW = 8.8224 1-4 EEL = 9.6391 RESTRAINT =
0.0000

NA:
   NSTEP ENERGY RMS GMAX NAME NUMBER
   4822 5.3636E+01 8.8686E-05 2.9553E-04 C8 24

 BOND = 2.6753 ANGLE = 25.7361 DIHED =
17.3886
 VDWAALS = -6.8103 EEL = -194.3192 HBOND =
0.0000
 1-4 VDW = 10.7541 1-4 EEL = 198.2115 RESTRAINT =
0.0000

 Basically the difference is due to 1-4 EEL in NA. The two nucleotides are
very similar, except that NA has a triangular ring, which I suppose would
add some steric interactions. At the end, please find the missing
parameters that parmcheck comes up with. If the problem is with these
parameters, it is strange that it only shows up in 1-4 EEL.

  Best wishes

  Mey

remark goes here
MASS

BOND
cx-na 334.70 1.456 same as c3-na

ANGLE
c3-cx-hc 33.311 117.235 Calculated with empirical approach
c3-c3-o 62.686 116.465 Calculated with empirical approach
cx-cx-na 65.300 116.300 same as cx-cx-n3
c3-cx-na 65.800 112.590 same as c3-c3-na
h1-c3-cx 46.700 111.350 same as cx-c3-hc
oh-c3-cx 67.700 109.430 same as c3-c3-oh
cx-na-cc 62.600 125.090 same as c3-na-cc
cx-na-ca 63.100 124.360 same as c3-na-ca

DIHE
c3-c3-cx-hc 1 0.156 0.000 3.000 same as X
-c3-c3-X
c3-c3-cx-cx 1 0.156 0.000 3.000 same as X
-c3-c3-X
hc-c3-cx-hc 1 0.156 0.000 3.000 same as X
-c3-c3-X
hc-c3-cx-cx 1 0.156 0.000 3.000 same as X
-c3-c3-X
cx-cx-c3-h1 1 0.156 0.000 3.000 same as X
-c3-c3-X
cx-cx-c3-oh 1 0.156 0.000 3.000 same as X
-c3-c3-X
cx-cx-na-cc 1 0.000 0.000 2.000 same as X
-c3-na-X
cx-cx-na-ca 1 0.000 0.000 2.000 same as X
-c3-na-X
c3-c3-cx-na 1 0.156 0.000 3.000 same as X
-c3-c3-X
c3-cx-na-cc 1 0.000 0.000 2.000 same as X
-c3-na-X
c3-cx-na-ca 1 0.000 0.000 2.000 same as X
-c3-na-X
h1-c3-cx-na 1 0.156 0.000 3.000 same as X
-c3-c3-X
oh-c3-cx-na 1 0.156 0.000 3.000 same as X
-c3-c3-X

IMPROPER
ca-cc-na-cx 1.1 180.0 2.0 Using default
value
h5-na-cc-nd 1.1 180.0 2.0 Using default
value
ca-ca-ca-nd 1.1 180.0 2.0 Using default
value
ca-nb-ca-nh 1.1 180.0 2.0 Using default
value
ca-hn-nh-hn 1.1 180.0 2.0 Using default
value
h5-nb-ca-nb 1.1 180.0 2.0 Using default
value
ca-na-ca-nb 1.1 180.0 2.0 Using default
value

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