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Joined: Oct 2017
Posts: 42
Forum Member
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OP
Forum Member
Joined: Oct 2017
Posts: 42 |
Hi, I am trying to build Di-alanine which I will solvate later. below is the snippet I am using to create di-alanine. Why am I getting error when all parameters are there in rtf and par files.
read sequence ALA 1
generate PRT setup first ACED last CT3
ic fill preserve
ic parameter
ic build
ic print
hbuild sele all end
NUMBER OF INTERNAL COORDINATES : 24
N I J K L R(I(J/K)) T(I(JK/KJ)) PHI T(JKL) R(KL)
1 1 CY 1 N 1 CA 1 C 1.3450 120.00 -60.00 107.00 1.4900
2 1 CY 1 CA 1 *N 1 HN 1.3450 120.00 180.00 117.00 0.9970
3 1 CAY 1 CY 1 N 1 CA 1.4900 116.50 180.00 120.00 1.4300
4 1 N 1 CAY 1 *CY 1 OY 1.3450 116.50 180.00 121.00 1.2300
5 1 OY 1 CY 1 CAY 1 HY1 1.2300 121.00 180.00 109.50 1.1110
6 1 OY 1 CY 1 CAY 1 HY2 1.2300 121.00 60.00 109.50 1.1110
7 1 OY 1 CY 1 CAY 1 HY3 1.2300 121.00 -60.00 109.50 1.1110
8 -99 ?? 1 CA 1 *N 1 HN 1.3551 126.49 180.00 115.42 0.9996
9 -99 ?? 1 N 1 CA 1 C 1.3551 126.49 180.00 114.44 1.5390
10 1 N 1 CA 1 C -99 ?? 1.4592 114.44 180.00 116.84 1.3558
11 -99 ?? 1 CA 1 *C 1 O 1.3558 116.84 180.00 122.52 1.2297
12 1 CA 1 C -99 ?? -99 ?? 1.5390 116.84 180.00 126.77 1.4613
13 1 N 1 C 1 *CA 1 CB 1.4592 114.44 123.23 111.09 1.5461
14 1 N 1 C 1 *CA 1 HA 1.4592 114.44 -120.45 106.39 1.0840
15 1 C 1 CA 1 CB 1 HB1 1.5390 111.09 177.25 109.60 1.1109
16 1 HB1 1 CA 1 *CB 1 HB2 1.1109 109.60 119.13 111.05 1.1119
17 1 HB1 1 CA 1 *CB 1 HB3 1.1109 109.60 -119.58 111.61 1.1114
18 1 N 1 CA 1 C 1 NT 1.4300 107.00 180.00 116.50 1.3450
19 1 NT 1 CA 1 *C 1 O 1.3450 116.50 180.00 121.00 1.2300
20 1 C 1 CAT 1 *NT 1 HNT 1.3450 120.00 180.00 117.00 0.9970
21 1 CA 1 C 1 NT 1 CAT 1.4900 116.50 180.00 120.00 1.4300
22 1 C 1 NT 1 CAT 1 HT1 1.3450 120.00 60.00 109.50 1.1110
23 1 C 1 NT 1 CAT 1 HT2 1.3450 120.00 180.00 109.50 1.1110
24 1 C 1 NT 1 CAT 1 HT3 1.3450 120.00 -60.00 109.50 1.1110
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WARNING FROM HBUILD:
Attempt to construct a hydrogen bonded to the atom PRT 1 ALA CAY with unknown coordinates.
*** LEVEL 0 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.
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Joined: Sep 2003
Posts: 8,660 Likes: 26
Forum Member
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Forum Member
Joined: Sep 2003
Posts: 8,660 Likes: 26 |
You need coordinates for at least 3 atoms which are bonded to each other; see IC SEED in the 'intcor' docs
Rick Venable
computational chemist
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