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AMBER Archive (2007)
Subject: Re: AMBER: RED-vIII fails
From: Jesper Soerensen (lists_at_jsx.dk)
Date: Tue Oct 30 2007 - 03:16:36 CST
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Files are attached, I figured I'd include all the data, as the file size
wasn't too different.
Thanks,
Jesper
On Mon, 2007-10-29 at 17:25 +0100, FyD wrote:
> Quoting Jesper Soerensen <lists_at_jsx.dk>:
>
> > I am trying to prepare parameters for a neutral C-terminal amino acid. I
> > have done as in the tutorial, but the program fails giving the following
> > message:
> >
> >> The RESP-A1 charges are being derived for ALL molecules...
> >> [ FAILED ]
> >> See the "output(1|2)_mm" file
> >
> > If I look at the output of "output2_mm" then at the end of the file it
> > says:
> >> Unit 3 Error on OPEN: qout1_mm
>
> Could you provide the end of the output1_mm and output2_mm files ?
> Let's say the last 100 lines...
>
> > And I have checked there is no file by that name. Have I done something
> > wrong? I have run all the QM (g03) calculations in RED, but I have
> > checked and made sure that they have all returned an optimized
> > structure. I have included the headers of the two files I am using.
>
> regards, Francois
>
>
> -----------------------------------------------------------------------
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-----------------------------------------------
Restrained ESP Fit 2.3 Amber 4.1
-----------------------------------------------
RESP-A1 project. RESP input generated by R.E.D.
-----------------------------------------------
inopt = 0 ioutopt = 1
nmol = 9 iqopt = 1
ihfree = 1 irstrnt = 1
iunits = 0 qwt = 0.00050000
%RESP-I-MULT_MOL, multiple-molecule run of 9 molecules
Reading input for molecule 1 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
1 6 0
2 1 0
3 1 0
4 1 0
5 6 0
6 8 0
7 7 0
8 1 0
9 6 0
10 1 0
11 6 0
12 1 0
13 8 0
14 1 0
15 6 0
16 1 0
17 1 0
18 1 0
19 6 0
20 8 0
21 7 0
22 1 0
23 6 0
24 1 0
25 1 0
26 1 0
Reading input for molecule 2 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
27 6 0
28 1 0
29 1 0
30 1 0
31 6 0
32 8 0
33 7 0
34 1 0
35 6 0
36 1 0
37 6 0
38 1 0
39 8 0
40 1 0
41 6 0
42 1 0
43 1 0
44 1 0
45 6 0
46 8 0
47 7 0
48 1 0
49 6 0
50 1 0
51 1 0
52 1 0
Reading input for molecule 3 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
53 6 0
54 1 0
55 1 0
56 1 0
57 6 0
58 8 0
59 7 0
60 1 0
61 6 0
62 1 0
63 6 0
64 1 0
65 8 0
66 1 0
67 6 0
68 1 0
69 1 0
70 1 0
71 6 0
72 8 0
73 7 0
74 1 0
75 6 0
76 1 0
77 1 0
78 1 0
Reading input for molecule 4 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
79 6 0
80 1 0
81 1 0
82 1 0
83 6 0
84 8 0
85 7 0
86 1 0
87 6 0
88 1 0
89 6 0
90 1 0
91 8 0
92 1 0
93 6 0
94 1 0
95 1 0
96 1 0
97 6 0
98 8 0
99 7 0
100 1 0
101 6 0
102 1 0
103 1 0
104 1 0
Reading input for molecule 5 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
105 6 0
106 1 0
107 1 0
108 1 0
109 6 0
110 8 0
111 7 0
112 1 0
113 6 0
114 1 0
115 6 0
116 1 0
117 8 0
118 1 0
119 6 0
120 1 0
121 1 0
122 1 0
123 6 0
124 8 0
125 7 0
126 1 0
127 6 0
128 1 0
129 1 0
130 1 0
Reading input for molecule 6 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
131 6 0
132 1 0
133 1 0
134 1 0
135 6 0
136 8 0
137 7 0
138 1 0
139 6 0
140 1 0
141 6 0
142 1 0
143 8 0
144 1 0
145 6 0
146 1 0
147 1 0
148 1 0
149 6 0
150 8 0
151 7 0
152 1 0
153 6 0
154 1 0
155 1 0
156 1 0
Reading input for molecule 7 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
157 6 0
158 1 0
159 1 0
160 1 0
161 6 0
162 8 0
163 7 0
164 1 0
165 6 0
166 1 0
167 6 0
168 1 0
169 8 0
170 1 0
171 6 0
172 1 0
173 1 0
174 1 0
175 6 0
176 8 0
177 7 0
178 1 0
179 6 0
180 1 0
181 1 0
182 1 0
Reading input for molecule 8 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
183 6 0
184 1 0
185 1 0
186 1 0
187 6 0
188 8 0
189 7 0
190 1 0
191 6 0
192 1 0
193 6 0
194 1 0
195 8 0
196 1 0
197 6 0
198 1 0
199 1 0
200 1 0
201 6 0
202 8 0
203 7 0
204 1 0
205 6 0
206 1 0
207 1 0
208 1 0
Reading input for molecule 9 weight: 1.000
Acetic
Total charge (ich): 0
Number of centers: 8
209 6 0
210 1 0
211 1 0
212 1 0
213 6 0
214 8 0
215 8 0
216 1 0
1 1 1 2 1 3 1 4 1 5 1 6
-----------------------------------------------
Restrained ESP Fit 2.3 Amber 4.1
-----------------------------------------------
RESP-A1 project. RESP input generated by R.E.D.
-----------------------------------------------
inopt = 0 ioutopt = 1
nmol = 9 iqopt = 2
ihfree = 1 irstrnt = 1
iunits = 0 qwt = 0.00100000
%RESP-I-MULT_MOL, multiple-molecule run of 9 molecules
Reading input for molecule 1 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
1 6 -1
2 1 -1
3 1 -1
4 1 -1
5 6 -1
6 8 -1
7 7 -1
8 1 -1
9 6 -1
10 1 -1
11 6 -1
12 1 -1
13 8 -1
14 1 -1
15 6 0
16 1 0
17 1 16
18 1 16
19 6 -1
20 8 -1
21 7 -1
22 1 -1
23 6 -1
24 1 -1
25 1 -1
26 1 -1
Reading input for molecule 2 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
27 6 -1
28 1 -1
29 1 -1
30 1 -1
31 6 -1
32 8 -1
33 7 -1
34 1 -1
35 6 -1
36 1 -1
37 6 -1
38 1 -1
39 8 -1
40 1 -1
41 6 0
42 1 0
43 1 16
44 1 16
45 6 -1
46 8 -1
47 7 -1
48 1 -1
49 6 -1
50 1 -1
51 1 -1
52 1 -1
Reading input for molecule 3 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
53 6 -1
54 1 -1
55 1 -1
56 1 -1
57 6 -1
58 8 -1
59 7 -1
60 1 -1
61 6 -1
62 1 -1
63 6 -1
64 1 -1
65 8 -1
66 1 -1
67 6 0
68 1 0
69 1 16
70 1 16
71 6 -1
72 8 -1
73 7 -1
74 1 -1
75 6 -1
76 1 -1
77 1 -1
78 1 -1
Reading input for molecule 4 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
79 6 -1
80 1 -1
81 1 -1
82 1 -1
83 6 -1
84 8 -1
85 7 -1
86 1 -1
87 6 -1
88 1 -1
89 6 -1
90 1 -1
91 8 -1
92 1 -1
93 6 0
94 1 0
95 1 16
96 1 16
97 6 -1
98 8 -1
99 7 -1
100 1 -1
101 6 -1
102 1 -1
103 1 -1
104 1 -1
Reading input for molecule 5 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
105 6 -1
106 1 -1
107 1 -1
108 1 -1
109 6 -1
110 8 -1
111 7 -1
112 1 -1
113 6 -1
114 1 -1
115 6 -1
116 1 -1
117 8 -1
118 1 -1
119 6 0
120 1 0
121 1 16
122 1 16
123 6 -1
124 8 -1
125 7 -1
126 1 -1
127 6 -1
128 1 -1
129 1 -1
130 1 -1
Reading input for molecule 6 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
131 6 -1
132 1 -1
133 1 -1
134 1 -1
135 6 -1
136 8 -1
137 7 -1
138 1 -1
139 6 -1
140 1 -1
141 6 -1
142 1 -1
143 8 -1
144 1 -1
145 6 0
146 1 0
147 1 16
148 1 16
149 6 -1
150 8 -1
151 7 -1
152 1 -1
153 6 -1
154 1 -1
155 1 -1
156 1 -1
Reading input for molecule 7 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
157 6 -1
158 1 -1
159 1 -1
160 1 -1
161 6 -1
162 8 -1
163 7 -1
164 1 -1
165 6 -1
166 1 -1
167 6 -1
168 1 -1
169 8 -1
170 1 -1
171 6 0
172 1 0
173 1 16
174 1 16
175 6 -1
176 8 -1
177 7 -1
178 1 -1
179 6 -1
180 1 -1
181 1 -1
182 1 -1
Reading input for molecule 8 weight: 1.000
Threonine-dipeptide,
Total charge (ich): 0
Number of centers: 26
183 6 -1
184 1 -1
185 1 -1
186 1 -1
187 6 -1
188 8 -1
189 7 -1
190 1 -1
191 6 -1
192 1 -1
193 6 -1
194 1 -1
195 8 -1
196 1 -1
197 6 0
198 1 0
199 1 16
200 1 16
201 6 -1
202 8 -1
203 7 -1
204 1 -1
205 6 -1
206 1 -1
207 1 -1
208 1 -1
Reading input for molecule 9 weight: 1.000
Acetic
Total charge (ich): 0
Number of centers: 8
209 6 -1
210 1 -1
211 1 -1
212 1 -1
213 6 -1
214 8 -1
215 8 -1
216 1 -1
Unit 3 Error on OPEN: qout1_mm
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
- Next message: varsha rani: "AMBER: anal problem"
- Previous message: Seongeun Yang: "Re: AMBER: &dipole input and some questions on using polarizable force fields"
- In reply to: FyD: "Re: AMBER: RED-vIII fails"
- Next in thread: FyD: "Re: AMBER: RED-vIII fails"
- Reply: FyD: "Re: AMBER: RED-vIII fails"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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