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IC build not generating ic table
#38049 08/18/20 06:43 AM
Joined: Oct 2017
Posts: 42
R
Rohit Offline OP
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R
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.

Code
read sequence ALA 1
generate PRT setup first ACED last CT3

ic fill preserve
ic parameter
ic build
ic print
hbuild sele all end

Code
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.


Re: IC build not generating ic table
Rohit #38053 08/18/20 02:52 PM
Joined: Sep 2003
Posts: 8,503
rmv Offline
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Posts: 8,503
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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