AMBER Archive (2008)

Subject: AMBER: antechamber

From: dipti lele (diptisl86_at_gmail.com)
Date: Sat Oct 11 2008 - 23:43:33 CDT

Hello all,,

  I wish to do membrane simulation using AMBER force field. Main component
of the membrane is POPE. I tried running antechamber for the first time to
generate the parameters for POPE. I satisfied all the valence by adding
hydrogen. But even then I am getting the error.

 The command I used is
antechamber -i pope_hyd.pdb -fi pdb -o pope.prepin -fo prepi -c bcc

The error I am getting :

The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically

Info: the atom number exceeds the MAXATOM, reallocate memory automatically
For atom[26]:O32, the best APS is not zero, exit
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase the computer time
Error: cannot run "/root/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c
properly, exit

I am using POPE molecule generated by the membrane package of VMD.

Here is the pdb file :
ATOM 1 N POPE 1 -41.156 -40.019 21.411 1.00 0.00 L11
N
ATOM 2 HN1 POPE 1 -41.886 -39.572 20.758 1.00 0.00 L11
H
ATOM 3 HN2 POPE 1 -40.177 -39.801 21.099 1.00 0.00 L11
H
ATOM 4 HN3 POPE 1 -41.156 -41.013 21.373 1.00 0.00 L11
H
ATOM 5 C12 POPE 1 -41.099 -39.399 22.783 1.00 0.00 L11
C
ATOM 6 H12A POPE 1 -40.126 -39.741 23.160 1.00 0.00 L11
H
ATOM 7 H12B POPE 1 -41.966 -39.751 23.383 1.00 0.00 L11
H
ATOM 8 C11 POPE 1 -41.110 -37.812 22.777 1.00 0.00 L11
C
ATOM 9 H11A POPE 1 -42.184 -37.491 22.579 1.00 0.00 L11
H
ATOM 10 H11B POPE 1 -40.864 -37.541 23.885 1.00 0.00 L11
H
ATOM 11 P POPE 1 -38.784 -37.508 21.444 1.00 0.00 L11
P
ATOM 12 O13 POPE 1 -38.185 -36.236 21.040 1.00 0.00 L11
O
ATOM 13 O14 POPE 1 -38.147 -38.252 22.523 1.00 0.00 L11
O
ATOM 14 O11 POPE 1 -38.836 -38.466 20.192 1.00 0.00 L11
O
ATOM 15 O12 POPE 1 -40.214 -37.156 21.774 1.00 0.00 L11
O
ATOM 16 C1 POPE 1 -39.269 -38.039 18.920 1.00 0.00 L11
C
ATOM 17 HA POPE 1 -40.353 -37.741 18.936 1.00 0.00 L11
H
ATOM 18 HB POPE 1 -38.772 -37.074 18.607 1.00 0.00 L11
H
ATOM 19 C2 POPE 1 -39.283 -39.144 17.835 1.00 0.00 L11
C
ATOM 20 HS POPE 1 -38.365 -39.684 17.941 1.00 0.00 L11
H
ATOM 21 O21 POPE 1 -39.458 -38.583 16.505 1.00 0.00 L11
O
ATOM 22 C21 POPE 1 -38.853 -39.400 15.490 1.00 0.00 L11
C
ATOM 23 O22 POPE 1 -38.252 -40.405 15.743 1.00 0.00 L11
O
ATOM 24 C22 POPE 1 -39.385 -39.069 14.110 1.00 0.00 L11
C
ATOM 25 H2R POPE 1 -40.507 -39.133 14.107 1.00 0.00 L11
H
ATOM 26 H2S POPE 1 -38.947 -38.013 13.795 1.00 0.00 L11
H
ATOM 27 C3 POPE 1 -40.456 -40.220 18.074 1.00 0.00 L11
C
ATOM 28 HX POPE 1 -40.301 -40.906 17.250 1.00 0.00 L11
H
ATOM 29 HY POPE 1 -40.316 -40.706 19.063 1.00 0.00 L11
H
ATOM 30 O31 POPE 1 -41.832 -39.634 18.135 1.00 0.00 L11
O
ATOM 31 C31 POPE 1 -42.818 -40.394 17.690 1.00 0.00 L11
C
ATOM 32 O32 POPE 1 -42.692 -41.570 17.396 1.00 0.00 L11
O
ATOM 33 C32 POPE 1 -44.181 -39.750 17.696 1.00 0.00 L11
C
ATOM 34 H2X POPE 1 -44.834 -40.468 17.138 1.00 0.00 L11
H
ATOM 35 H2Y POPE 1 -44.440 -39.596 18.744 1.00 0.00 L11
H
ATOM 36 C23 POPE 1 -39.011 -40.027 12.960 1.00 0.00 L11
C
ATOM 37 H3R POPE 1 -37.937 -40.203 12.934 1.00 0.00 L11
H
ATOM 38 H3S POPE 1 -39.583 -40.984 13.282 1.00 0.00 L11
H
ATOM 39 C24 POPE 1 -39.507 -39.374 11.583 1.00 0.00 L11
C
ATOM 40 H4R POPE 1 -40.619 -39.128 11.487 1.00 0.00 L11
H
ATOM 41 H4S POPE 1 -38.967 -38.403 11.432 1.00 0.00 L11
H
ATOM 42 C25 POPE 1 -39.181 -40.223 10.335 1.00 0.00 L11
C
ATOM 43 H5R POPE 1 -38.116 -40.201 10.186 1.00 0.00 L11
H
ATOM 44 H5S POPE 1 -39.607 -41.237 10.545 1.00 0.00 L11
H
ATOM 45 C26 POPE 1 -39.862 -39.719 9.030 1.00 0.00 L11
C
ATOM 46 H6R POPE 1 -40.949 -39.755 9.215 1.00 0.00 L11
H
ATOM 47 H6S POPE 1 -39.511 -38.720 8.693 1.00 0.00 L11
H
ATOM 48 C27 POPE 1 -39.600 -40.724 7.885 1.00 0.00 L11
C
ATOM 49 H7R POPE 1 -38.581 -40.571 7.487 1.00 0.00 L11
H
ATOM 50 H7S POPE 1 -39.759 -41.820 8.089 1.00 0.00 L11
H
ATOM 51 C28 POPE 1 -40.590 -40.583 6.648 1.00 0.00 L11
C
ATOM 52 H8R POPE 1 -41.586 -40.726 7.011 1.00 0.00 L11
H
ATOM 53 H8S POPE 1 -40.524 -39.529 6.198 1.00 0.00 L11
H
ATOM 54 C29 POPE 1 -40.349 -41.605 5.485 1.00 0.00 L11
C
ATOM 55 H91 POPE 1 -40.449 -42.607 5.859 1.00 0.00 L11
H
ATOM 56 C210 POPE 1 -40.166 -41.275 4.189 1.00 0.00 L11
C
ATOM 57 H101 POPE 1 -39.930 -42.067 3.517 1.00 0.00 L11
H
ATOM 58 C211 POPE 1 -40.053 -39.930 3.535 1.00 0.00 L11
C
ATOM 59 H11R POPE 1 -41.029 -39.487 3.286 1.00 0.00 L11
H
ATOM 60 H11S POPE 1 -39.795 -39.202 4.268 1.00 0.00 L11
H
ATOM 61 C212 POPE 1 -39.240 -39.657 2.248 1.00 0.00 L11
C
ATOM 62 H12R POPE 1 -39.365 -38.570 1.878 1.00 0.00 L11
H
ATOM 63 H12S POPE 1 -38.198 -39.887 2.393 1.00 0.00 L11
H
ATOM 64 C213 POPE 1 -39.794 -40.454 1.025 1.00 0.00 L11
C
ATOM 65 H13R POPE 1 -39.884 -41.578 1.311 1.00 0.00 L11
H
ATOM 66 H13S POPE 1 -40.854 -40.172 0.844 1.00 0.00 L11
H
ATOM 67 C214 POPE 1 -38.927 -40.193 -0.235 1.00 0.00 L11
C
ATOM 68 H14R POPE 1 -38.782 -39.107 -0.329 1.00 0.00 L11
H
ATOM 69 H14S POPE 1 -37.961 -40.651 -0.166 1.00 0.00 L11
H
ATOM 70 C215 POPE 1 -39.570 -40.799 -1.495 1.00 0.00 L11
C
ATOM 71 H15R POPE 1 -39.900 -41.808 -1.342 1.00 0.00 L11
H
ATOM 72 H15S POPE 1 -40.408 -40.144 -1.669 1.00 0.00 L11
H
ATOM 73 C216 POPE 1 -38.863 -40.455 -2.844 1.00 0.00 L11
C
ATOM 74 H16R POPE 1 -38.689 -39.394 -2.809 1.00 0.00 L11
H
ATOM 75 H16S POPE 1 -37.830 -40.968 -2.816 1.00 0.00 L11
H
ATOM 76 C217 POPE 1 -39.767 -40.781 -4.018 1.00 0.00 L11
C
ATOM 77 H17R POPE 1 -40.028 -41.872 -3.772 1.00 0.00 L11
H
ATOM 78 H17S POPE 1 -40.715 -40.266 -3.938 1.00 0.00 L11
H
ATOM 79 C218 POPE 1 -39.051 -40.735 -5.410 1.00 0.00 L11
C
ATOM 80 H18R POPE 1 -39.733 -40.891 -6.234 1.00 0.00 L11
H
ATOM 81 H18S POPE 1 -38.621 -39.702 -5.548 1.00 0.00 L11
H
ATOM 82 H18T POPE 1 -38.171 -41.361 -5.399 1.00 0.00 L11
H
ATOM 83 C33 POPE 1 -44.217 -38.468 16.891 1.00 0.00 L11
C
ATOM 84 H3X POPE 1 -45.207 -37.948 16.968 1.00 0.00 L11
H
ATOM 85 H3Y POPE 1 -43.443 -37.897 17.433 1.00 0.00 L11
H
ATOM 86 C34 POPE 1 -43.794 -38.628 15.414 1.00 0.00 L11
C
ATOM 87 H4X POPE 1 -42.704 -38.609 15.374 1.00 0.00 L11
H
ATOM 88 H4Y POPE 1 -44.042 -39.609 15.024 1.00 0.00 L11
H
ATOM 89 C35 POPE 1 -44.405 -37.606 14.455 1.00 0.00 L11
C
ATOM 90 H5X POPE 1 -45.456 -37.926 14.330 1.00 0.00 L11
H
ATOM 91 H5Y POPE 1 -44.411 -36.575 14.889 1.00 0.00 L11
H
ATOM 92 C36 POPE 1 -43.733 -37.815 13.015 1.00 0.00 L11
C
ATOM 93 H6X POPE 1 -42.805 -37.258 12.892 1.00 0.00 L11
H
ATOM 94 H6Y POPE 1 -43.404 -38.860 12.953 1.00 0.00 L11
H
ATOM 95 C37 POPE 1 -44.644 -37.636 11.876 1.00 0.00 L11
C
ATOM 96 H7X POPE 1 -45.560 -38.242 11.901 1.00 0.00 L11
H
ATOM 97 H7Y POPE 1 -44.788 -36.567 11.756 1.00 0.00 L11
H
ATOM 98 C38 POPE 1 -43.841 -37.975 10.665 1.00 0.00 L11
C
ATOM 99 H8X POPE 1 -42.891 -37.468 10.770 1.00 0.00 L11
H
ATOM 100 H8Y POPE 1 -43.662 -39.030 10.630 1.00 0.00 L11
H
ATOM 101 C39 POPE 1 -44.472 -37.574 9.339 1.00 0.00 L11
C
ATOM 102 H9X POPE 1 -45.457 -38.066 9.259 1.00 0.00 L11
H
ATOM 103 H9Y POPE 1 -44.785 -36.445 9.408 1.00 0.00 L11
H
ATOM 104 C310 POPE 1 -43.621 -37.853 8.172 1.00 0.00 L11
C
ATOM 105 H10X POPE 1 -42.735 -37.137 8.031 1.00 0.00 L11
H
ATOM 106 H10Y POPE 1 -43.204 -38.831 8.312 1.00 0.00 L11
H
ATOM 107 C311 POPE 1 -44.353 -37.582 6.852 1.00 0.00 L11
C
ATOM 108 H11X POPE 1 -45.222 -38.193 6.891 1.00 0.00 L11
H
ATOM 109 H11Y POPE 1 -44.763 -36.501 6.928 1.00 0.00 L11
H
ATOM 110 C312 POPE 1 -43.606 -37.786 5.543 1.00 0.00 L11
C
ATOM 111 H12X POPE 1 -42.813 -37.000 5.452 1.00 0.00 L11
H
ATOM 112 H12Y POPE 1 -42.993 -38.702 5.647 1.00 0.00 L11
H
ATOM 113 C313 POPE 1 -44.498 -37.789 4.333 1.00 0.00 L11
C
ATOM 114 H13X POPE 1 -45.328 -38.561 4.447 1.00 0.00 L11
H
ATOM 115 H13Y POPE 1 -45.013 -36.824 4.416 1.00 0.00 L11
H
ATOM 116 C314 POPE 1 -43.712 -37.794 3.097 1.00 0.00 L11
C
ATOM 117 H14X POPE 1 -42.964 -36.960 3.222 1.00 0.00 L11
H
ATOM 118 H14Y POPE 1 -43.226 -38.757 2.997 1.00 0.00 L11
H
ATOM 119 C315 POPE 1 -44.585 -37.376 1.957 1.00 0.00 L11
C
ATOM 120 H15X POPE 1 -45.085 -38.342 1.763 1.00 0.00 L11
H
ATOM 121 H15Y POPE 1 -45.313 -36.590 2.259 1.00 0.00 L11
H
ATOM 122 C316 POPE 1 -43.767 -36.911 0.728 1.00 0.00 L11
C
ATOM 123 H16X POPE 1 -43.503 -37.755 0.104 1.00 0.00 L11
H
ATOM 124 H16Y POPE 1 -44.292 -36.264 0.022 1.00 0.00 L11
H
ATOM 125 H16Z POPE 1 -42.725 -36.486 1.075 1.00 0.00 L11
H

Could you guide me in this matter. I am not able to find the exact problem.
Is it that the molecule size is very large,

Thanking you...

With Regards, 

-- 
Deepti Lele,
NII, New Delhi.

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