This is what the printtypes command give me:
RDPARM MENU: printtypes
NOTE: if either A or C is zero (*), we cannot infer
the value of r* or epsilon and assume zero...
Type r* eps
n1 1.8240 0.1700
c3 1.9080 0.1094
h1 1.3870 0.0157
hn 0.6000 0.0157
c2 1.9080 0.0860
o 1.6612 0.2100
hc 1.4870 0.0157
ha 1.4590 0.0150
There are type n, and n3 that are missing.
Why is the printtype command giving me R* and epsilon parameters? what happened
to missing n and n3?
These types do exist, as shown when I type the command atoms :1-2,58 (residues
comprising all kinds of types in my macromolecule)
RDPARM MENU: atoms :1-2,58
Mask [:1-2,58] represents 93 atoms
Number: Atom Charge Mass ( Residue ) Type Tree
1: N73 -0.36852 14.0 ( 1:CEN ) n1 M
2: C61 -0.11857 12.0 ( 1:CEN ) c3 M
3: H62 0.15739 1.0 ( 1:CEN ) h1 E
4: H63 0.15739 1.0 ( 1:CEN ) h1 E
5: C49 -0.11670 12.0 ( 1:CEN ) c3 M
6: H50 0.17474 1.0 ( 1:CEN ) h1 E
7: H51 0.17474 1.0 ( 1:CEN ) h1 E
8: N41 -0.50332 14.0 ( 1:CEN ) n M
9: H42 0.23683 1.0 ( 1:CEN ) hn E
10: C33 0.45405 12.0 ( 1:CEN ) c2 M
11: O34 -0.48122 16.0 ( 1:CEN ) o E
12: C21 -0.19460 12.0 ( 1:CEN ) c3 M
13: H22 0.12265 1.0 ( 1:CEN ) hc E
14: H23 0.12265 1.0 ( 1:CEN ) hc E
15: C9 -0.11921 12.0 ( 1:CEN ) c3 M
16: H10 0.15085 1.0 ( 1:CEN ) h1 E
17: H11 0.15085 1.0 ( 1:CEN ) h1 E
18: N7 -0.23776 14.0 ( 1:CEN ) n3 M
19: C12 -0.11921 12.0 ( 1:CEN ) c3 3
20: H13 0.15085 1.0 ( 1:CEN ) h1 E
21: H14 0.15085 1.0 ( 1:CEN ) h1 E
22: C24 -0.19460 12.0 ( 1:CEN ) c3 3
23: H25 0.12265 1.0 ( 1:CEN ) hc E
24: H26 0.12265 1.0 ( 1:CEN ) hc E
25: C35 0.45405 12.0 ( 1:CEN ) c2 B
26: O36 -0.48122 16.0 ( 1:CEN ) o E
27: N43 -0.50332 14.0 ( 1:CEN ) n B
28: H44 0.23683 1.0 ( 1:CEN ) hn E
29: C52 -0.11670 12.0 ( 1:CEN ) c3 3
30: H53 0.17474 1.0 ( 1:CEN ) h1 E
31: H54 0.17474 1.0 ( 1:CEN ) h1 E
32: C64 -0.11857 12.0 ( 1:CEN ) c3 3
33: H65 0.15739 1.0 ( 1:CEN ) h1 E
34: H66 0.15739 1.0 ( 1:CEN ) h1 E
35: N74 -0.36852 14.0 ( 1:CEN ) n1 E
36: C1 -0.08693 12.0 ( 1:CEN ) c3 M
37: H2 0.16234 1.0 ( 1:CEN ) h1 E
38: H3 0.16235 1.0 ( 1:CEN ) h1 E
39: C4 -0.08693 12.0 ( 1:CEN ) c3 M
40: H5 0.16234 1.0 ( 1:CEN ) h1 E
41: H6 0.16234 1.0 ( 1:CEN ) h1 E
42: N8 -0.23776 14.0 ( 1:CEN ) n3 M
43: C18 -0.11921 12.0 ( 1:CEN ) c3 3
44: H19 0.15085 1.0 ( 1:CEN ) h1 E
45: H20 0.15085 1.0 ( 1:CEN ) h1 E
46: C30 -0.19460 12.0 ( 1:CEN ) c3 3
47: H31 0.12265 1.0 ( 1:CEN ) hc E
48: H32 0.12265 1.0 ( 1:CEN ) hc E
49: C39 0.45405 12.0 ( 1:CEN ) c2 B
50: O40 -0.48122 16.0 ( 1:CEN ) o E
51: N47 -0.50332 14.0 ( 1:CEN ) n B
52: H48 0.23683 1.0 ( 1:CEN ) hn E
53: C58 -0.11670 12.0 ( 1:CEN ) c3 3
54: H59 0.17474 1.0 ( 1:CEN ) h1 E
55: H60 0.17474 1.0 ( 1:CEN ) h1 E
56: C70 -0.11857 12.0 ( 1:CEN ) c3 3
57: H71 0.15739 1.0 ( 1:CEN ) h1 E
58: H72 0.15739 1.0 ( 1:CEN ) h1 E
59: N76 -0.36852 14.0 ( 1:CEN ) n1 E
60: C15 -0.11921 12.0 ( 1:CEN ) c3 M
61: H16 0.15085 1.0 ( 1:CEN ) h1 E
62: H17 0.15085 1.0 ( 1:CEN ) h1 E
63: C27 -0.19460 12.0 ( 1:CEN ) c3 M
64: H28 0.12265 1.0 ( 1:CEN ) hc E
65: H29 0.12265 1.0 ( 1:CEN ) hc E
66: C37 0.45405 12.0 ( 1:CEN ) c2 M
67: O38 -0.48122 16.0 ( 1:CEN ) o E
68: N45 -0.50332 14.0 ( 1:CEN ) n M
69: H46 0.23683 1.0 ( 1:CEN ) hn E
70: C55 -0.11670 12.0 ( 1:CEN ) c3 M
71: H56 0.17474 1.0 ( 1:CEN ) h1 E
72: H57 0.17474 1.0 ( 1:CEN ) h1 E
73: C67 -0.11857 12.0 ( 1:CEN ) c3 M
74: H68 0.15739 1.0 ( 1:CEN ) h1 E
75: H69 0.15739 1.0 ( 1:CEN ) h1 E
76: N75 -0.36852 14.0 ( 1:CEN ) n1 M
77: C1 -0.11921 12.0 ( 2:SPA ) c2 M
78: H2 0.15085 1.0 ( 2:SPA ) ha E
79: H3 0.15085 1.0 ( 2:SPA ) ha E
80: C4 -0.19460 12.0 ( 2:SPA ) c3 M
81: H5 0.12265 1.0 ( 2:SPA ) hc E
82: H6 0.12265 1.0 ( 2:SPA ) hc E
83: C7 0.45405 12.0 ( 2:SPA ) c2 M
84: O8 -0.48122 16.0 ( 2:SPA ) o E
85: N9 -0.50332 14.0 ( 2:SPA ) n M
86: H10 0.23683 1.0 ( 2:SPA ) hn E
87: C11 -0.11670 12.0 ( 2:SPA ) c3 M
88: H12 0.17474 1.0 ( 2:SPA ) h1 E
89: H13 0.17474 1.0 ( 2:SPA ) h1 E
90: C14 -0.11857 12.0 ( 2:SPA ) c3 M
91: H15 0.15739 1.0 ( 2:SPA ) h1 E
92: H16 0.15739 1.0 ( 2:SPA ) h1 E
93: N17 -0.36852 14.0 ( 2:SPA ) n1 M
Thanks for any clarification on this "printtypes" command.
regards
________________________________
From: Thomas Cheatham III <tec3.utah.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tue, August 3, 2010 12:24:40 AM
Subject: Re: [AMBER] RDPARM
> NTYPES is 8 (number of atom types)
...
>
> My macromelcule parameters were created with antechamber.
> Two points seem strange here:
> 1) the (number of atom types) rdparm says it is 8 although i know that there
>are
>
> 10!
Does the "printtypes" command show parameters for 10 different types?
> 2) NHB is 0 , does this mean that there are no H bond parameters available
> for the molecule?
Most of the force fields since very early ones do not contain explicit
"extra" hydrogen bonding potentials (i.e. 10-12) instead using
electrostatics and standard vdw to represent the h-bond.
--tec3
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Received on Tue Aug 03 2010 - 09:00:03 PDT
