hello computer people.
i am having the largest problems ever with creation of sensible prmtop/inpcrd files for the carbohydrate - sleX. i have used Homans carbohydrate parameters and with both parm91X.dat and parm94.dat, and while xleap produces prmtop/inpcrd files without any fuss, when i try to make a pdb file using the ambpdb function, i get the following message:
fmt: read unexpected character
apparent state: unit 10 named sialyl.prmtop
last format: (5E16.8)
Unit 10 is a sequential formatted external file
*** Execution Terminated (115) ***
- i just don't get it. do you??
thanks in advance.
amesh patel
From s.j.hughes_at_ic.ac.uk 27 Feb 2002 15:28:46 +0000
Message-id: <1014823726.10301.9.camel.calculus.ch.ic.ac.uk>
Date: 27 Feb 2002 15:28:46 +0000
From: samantha hughes <s.j.hughes_at_ic.ac.uk>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: Cholesterol PREP file
In-Reply-to: <Pine.SOL.4.43.0202251130560.19255-100000.easy>
Hi All,
I know that PREP is no longer supported, but figure that there are bound
to be people on the list who can help me with this. Does anyone have a
PREP file for cholesterol that they could give me or alternatively tell
me where I am going wrong in my attempts ? I am really struggling to
create a PREP input file for cholesterol that works properly. I have the
crystal structure coordinates, and am using the CHANGE option to read
these in (rather than laboriously figuring out the internal
coordinates). The file runs through PREP properly, but causes a
segmentation fault in LINK. If I load the AMBER PREP file into xLeap,
all of the atoms are at the same point in space (despite the PREP output
report being sensible). I'm including the file to see if anyone can
point out where I am going wrong.I can't find any examples of using the
CHANGE option in the amber5 demo directory.
I know that I could use LEaP, but have good reason for using the PLEP
method instead.
Thanks for any help,
Samantha
>>------------------------------------------------
0 0 2
Cholesterol
cho.res
CHO INT 0
CHANGE OMIT DU BEG
0.0
1 DUMM DU M 0.000 00.000 0.000
2 DUMM DU M 0.000 00.000 0.000
3 DUMM DU M 0.000 00.000 0.000
4 O1 OH M 3.489 13.841 5.662
5 H29 HO E 2.608 13.773 6.129
6 C3 CT M 3.983 12.509 5.362
7 H34 H1 E 3.329 12.036 4.772
8 C2 CT M 5.282 12.557 4.672
9 H32 HC E 5.171 13.065 3.818
10 H33 HC E 5.938 13.032 5.259
11 C1 CT M 5.789 11.170 4.371
12 H30 HC E 6.693 11.230 3.948
13 H31 HC E 5.158 10.712 3.745
14 C10 CT M 5.930 10.261 5.621
15 C19 CT 3 7.059 10.802 6.558
16 H55 HC E 7.927 10.813 6.062
17 H56 HC E 7.141 10.209 7.359
18 H57 HC E 6.832 11.730 6.853
19 C9 CT M 6.256 8.806 5.169
20 H41 HC E 5.564 8.708 4.454
21 C11 CT M 7.635 8.646 4.518
22 H42 HC E 8.343 8.942 5.159
23 H43 HC E 7.680 9.205 3.690
24 C12 CT M 7.990 7.202 4.135
25 H44 HC E 8.940 7.163 3.825
26 H45 HC E 7.387 6.894 3.399
27 C13 CT M 7.818 6.230 5.313
28 C18 CT 3 8.839 6.546 6.384
29 H52 HC E 9.760 6.450 6.006
30 H53 HC E 8.726 5.913 7.150
31 H54 HC E 8.707 7.484 6.705
32 C17 CT M 7.779 4.723 4.956
33 H51 HC E 7.202 4.711 4.140
34 C20 CT M 9.134 3.952 4.701
35 H58 HC E 9.656 3.903 5.553
36 C21 CT 3 9.950 4.638 3.641
37 H59 HC E 10.793 4.123 3.483
38 H60 HC E 10.177 5.564 3.942
39 H61 HC E 9.424 4.684 2.792
40 C22 CT M 8.835 2.499 4.309
41 H62 HC E 8.325 2.483 3.449
42 H63 HC E 8.291 2.065 5.027
43 C23 CT M 10.067 1.643 4.130
44 H64 HC E 10.610 1.660 4.970
45 H65 HC E 10.614 1.999 3.373
46 C24 CT M 9.657 0.183 3.771
47 H66 HC E 8.871 0.199 3.153
48 H67 HC E 9.413 -0.310 4.606
49 C25 CT M 10.674 -0.750 3.095
50 H68 HC E 10.875 -0.414 2.175
51 C26 CT 3 11.736 -0.708 4.028
52 H69 HC E 12.042 0.237 4.143
53 H70 HC E 12.496 -1.266 3.694
54 H71 HC E 11.422 -1.066 4.907
55 C27 CT M 9.992 -2.164 2.682
56 H72 HC E 10.650 -2.715 2.169
57 H73 HC E 9.187 -1.993 2.114
58 H74 HC E 9.718 -2.656 3.508
59 C16 CT 3 7.024 4.085 6.126
60 H49 HC E 6.444 3.354 5.766
61 H50 HC E 7.628 3.714 6.832
62 C15 CT 3 6.124 5.210 6.745
63 H47 HC E 5.156 4.960 6.725
64 H48 HC E 6.381 5.473 7.675
65 C14 CT B 6.366 6.380 5.801
66 H46 HC E 5.828 6.152 4.990
67 C8 CT B 5.992 7.778 6.284
68 H40 HC E 6.557 8.023 7.072
69 C7 CT 3 4.509 7.830 6.681
70 H38 HC E 3.982 7.351 5.979
71 H39 HC E 4.405 7.357 7.556
72 C6 CM B 4.005 9.244 6.810
73 H37 HC E 3.122 9.339 7.269
74 C5 CB S 4.636 10.311 6.371
75 C4 CT B 4.084 11.694 6.666
76 H35 HC E 3.172 11.578 7.059
77 H36 HC E 4.668 12.178 7.318
LOOP
C3 C4
C8 C9
C13 C14
C5 C10
DONE
STOP
>>--------------------------------------------
-------------------------------------------------------
Samantha Hughes
Department of Chemistry
Imperial College of Science, Technology and Medicine
Exhibition Road
London
SW7 2AY
-------------------------------------------------------
Received on Wed Feb 27 2002 - 06:43:23 PST
