AMBER Archive (2004)

Subject: Re: AMBER: segmentation fault when running parmchk

From: Chutintorn Punwong (punwong_at_uiuc.edu)
Date: Tue Jun 08 2004 - 13:07:45 CDT

Dear David,
I'm not sure you've got the attached prep file (jmins0.prep). How's it
going?
Thank you,
Chutintorn

> David A. Case wrote:
>
>>On Wed, Jun 02, 2004, Chutintorn Punwong wrote:
>>
>>
>>
>>>I have checked the AMBERHOME environment but I'm not sure what else I
>>>should look up. Could you give me some idea and also how to debug?
>>>
>>>
>>
>>Just my earlier suggestion (see below). Without that information, we can't
>>tell if the problem is with parmchk itself, or with antechamber.
>>
>>...dac
>>
>>
>>
>>>>Works for me, using either amber7 or amber8. You could send your
>>>>
>>>>
>> ^^^^^^^^^^^^^^^^^^^
>>
>>
>>>>jmins0.prep file...
>>>>
>>>>
>> ^^^^^^^^^^^^^^^^
>>
>>
>>
>
>------------------------------------------------------------------------
>
> 0 0 2
>
>This is a remark line
>molecule.res
>RET XYZ 0
>CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 C2 c3 M 3 2 1 1.540 111.208 180.000 -0.020
> 5 H14 h1 E 4 3 2 1.111 115.781 -180.000 0.078
> 6 H15 h1 E 4 3 2 1.110 114.884 -59.895 0.086
> 7 H16 h1 E 4 3 2 1.110 114.884 59.895 0.085
> 8 N1 n3 M 4 3 2 1.429 0.000 -90.000 -0.299
> 9 H17 hn E 8 4 3 0.972 115.405 45.000 0.310
> 10 C3 c2 M 8 4 3 1.314 123.581 45.000 0.432
> 11 H18 ha E 10 8 4 1.107 121.636 0.000 0.044
> 12 C4 cd M 10 8 4 1.413 124.879 -180.000 -0.433
> 13 H19 ha E 12 10 8 1.098 117.742 0.000 0.162
> 14 C5 cd M 12 10 8 1.372 124.675 180.000 0.187
> 15 C7 c3 3 14 12 10 1.470 121.766 0.000 -0.121
> 16 H21 hc E 15 14 12 1.100 111.964 120.370 0.089
> 17 H22 hc E 15 14 12 1.100 111.993 -120.326 0.089
> 18 H23 hc E 15 14 12 1.102 114.389 0.000 0.055
> 19 C6 cd M 14 12 10 1.424 119.229 -180.000 -0.272
> 20 H20 ha E 19 14 12 1.098 116.415 0.000 0.155
> 21 C8 cd M 19 14 12 1.362 126.416 180.000 0.065
> 22 H24 ha E 21 19 14 1.101 120.359 0.000 0.132
> 23 C9 cd M 21 19 14 1.418 123.600 -180.000 -0.238
> 24 H25 ha E 23 21 19 1.098 116.159 0.000 0.149
> 25 C10 cd M 23 21 19 1.361 125.295 180.000 0.079
> 26 C12 c3 3 25 23 21 1.468 121.886 0.000 -0.099
> 27 H27 hc E 26 25 23 1.100 112.087 120.264 0.077
> 28 H28 hc E 26 25 23 1.100 112.087 -120.264 0.077
> 29 H29 hc E 26 25 23 1.103 113.566 0.000 0.046
> 30 C11 cd M 25 23 21 1.445 119.503 -180.000 -0.193
> 31 H26 ha E 30 25 23 1.098 115.704 0.000 0.142
> 32 C13 c2 M 30 25 23 1.333 125.892 180.000 -0.128
> 33 H30 ha E 32 30 25 1.085 123.472 -180.000 0.138
> 34 H31 ha E 32 30 25 1.086 124.528 0.000 0.124
>
>
>LOOP
>
>IMPROPER
> C4 H18 C3 N1
> C3 C5 C4 H19
> C7 C4 C5 C6
> C5 C8 C6 H20
> C6 C9 C8 H24
> C8 C10 C9 H25
> C12 C9 C10 C11
> C13 C10 C11 H26
> C11 H30 C13 H31
>
>DONE
>STOP
>
>

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