AMBER Archive (2008)

Subject: Re: AMBER: autodock pdb to obtain parm with tleap

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Feb 27 2008 - 11:42:52 CST

Evidently, some atom names in your pdb and prepi files do not match. For
example, there are a couple hydrogen atoms have 4-letter names (such as
H271, H272 and H273) in pdb, while none hydrogen has 4-letter name in the
prepi file. I used your pdb file and ran antechamber to generate a prep
input file (antechamber -fi pdb -fo prepi -i input.pdb -o input.prepi -c
bcc). The prep input file looks good.

By the way, if you use resp charges and generate prepi directly from a
gaussian output, you need to provide atom names information to antechamber.
This is because gaussian output does not contain atom names information at
all. Here is the command you may try:

antechamber -fi gout -fo prepi -fa pdb -i mol.gout -o mol.prepi -a
mol.pdb-c resp -ao name

suppose your pdb file is mol.pdb and gaussian output file is mol.gout. "-ao
name" flag tells the program only replace the atom names information in gout
with those in mol.pdb.

Best

Junmei

On Wed, Feb 27, 2008 at 5:14 AM, Henar Martínez <henar_at_eis.uva.es> wrote:

> David A. Case escribió:
>
> On Tue, Feb 26, 2008, Henar Martínez wrote:
>
>
>
> Anybody know how to transform an autodock pdb file in a pdb one that
> tleap can use to generate the parm file.
> The problem is: tleap does not recognize the atom types of the autodock
> pdb file.
>
>
>
> We would need to see at least a little bit of the file to know what you are
> talking about. PDB files do not store atom type information, so it's hard
> to know what the real problem is.
>
> ...dac
>
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>
> I think the pdb file was in strange form, I send you again.
>
> REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0
> ATOM 1 C1 MOL 371 -10.209 -1.790 7.103 1.00 0.00
> conf C
> ATOM 2 H11 MOL 371 -9.283 -1.928 6.498 1.00 0.00
> conf H
> ATOM 3 H12 MOL 371 -10.155 -2.706 7.736 1.00 0.00
> conf H
> ATOM 4 C5 MOL 371 -10.110 -0.537 7.960 1.00 0.00
> conf C
> ATOM 5 H5 MOL 371 -10.961 -0.511 8.680 1.00 0.00
> conf H
> ATOM 6 C3 MOL 371 -10.131 0.718 7.107 1.00 0.00
> conf C
> ATOM 7 H3 MOL 371 -9.234 0.697 6.445 1.00 0.00
> conf H
> ATOM 8 C4 MOL 371 -11.381 0.847 6.208 1.00 0.00
> conf C
> ATOM 9 C2 MOL 371 -11.515 -0.483 5.397 1.00 0.00
> conf C
> ATOM 10 H2 MOL 371 -10.602 -0.509 4.758 1.00 0.00
> conf H
> ATOM 11 C15 MOL 371 -12.677 -0.515 4.397 1.00 0.00
> conf C
> ATOM 12 1H15 MOL 371 -13.656 -0.706 4.895 1.00 0.00
> conf H
> ATOM 13 2H15 MOL 371 -12.903 0.495 3.981 1.00 0.00
> conf H
> ATOM 14 C13 MOL 371 -12.378 -1.536 3.302 1.00 0.00
> conf C
> ATOM 15 1H13 MOL 371 -11.538 -1.181 2.660 1.00 0.00
> conf H
> ATOM 16 2H13 MOL 371 -13.201 -1.551 2.550 1.00 0.00
> conf H
> ATOM 17 C6 MOL 371 -11.463 -1.824 6.199 1.00 0.00
> conf C
> ATOM 18 C10 MOL 371 -11.359 -2.991 5.182 1.00 0.00
> conf C
> ATOM 19 C12 MOL 371 -10.754 -4.129 5.509 1.00 0.00
> conf C
> ATOM 20 H12 MOL 371 -10.274 -4.208 6.499 1.00 0.00
> conf H
> ATOM 21 C16 MOL 371 -10.699 -5.282 4.607 1.00 0.00
> conf C
> ATOM 22 H16 MOL 371 -10.453 -6.273 5.024 1.00 0.00
> conf H
> ATOM 23 C11 MOL 371 -12.094 -2.969 3.818 1.00 0.00
> conf C
> ATOM 24 C17 MOL 371 -11.234 -3.771 2.752 1.00 0.00
> conf C
> ATOM 25 C19 MOL 371 -9.859 -3.096 2.506 1.00 0.00
> conf C
> ATOM 26 1H19 MOL 371 -9.326 -3.049 3.484 1.00 0.00
> conf H
> ATOM 27 2H19 MOL 371 -9.947 -2.100 2.012 1.00 0.00
> conf H
> ATOM 28 3H19 MOL 371 -9.263 -3.602 1.711 1.00 0.00
> conf H
> ATOM 29 C25 MOL 371 -11.975 -3.836 1.391 1.00 0.00
> conf C
> ATOM 30 1H25 MOL 371 -13.077 -3.879 1.552 1.00 0.00
> conf H
> ATOM 31 2H25 MOL 371 -11.896 -2.859 0.860 1.00 0.00
> conf H
> ATOM 32 C24 MOL 371 -11.528 -4.977 0.473 1.00 0.00
> conf C
> ATOM 33 1H24 MOL 371 -10.489 -4.816 0.102 1.00 0.00
> conf H
> ATOM 34 2H24 MOL 371 -12.068 -4.948 -0.502 1.00 0.00
> conf H
> ATOM 35 C22 MOL 371 -11.674 -6.349 1.154 1.00 0.00
> conf C
> ATOM 36 C18 MOL 371 -10.934 -5.175 3.308 1.00 0.00
> conf C
> ATOM 37 C20 MOL 371 -10.773 -6.402 2.409 1.00 0.00
> conf C
> ATOM 38 H20 MOL 371 -11.097 -7.287 3.005 1.00 0.00
> conf H
> ATOM 39 C21 MOL 371 -9.284 -6.622 2.045 1.00 0.00
> conf C
> ATOM 40 1H21 MOL 371 -8.858 -5.694 1.596 1.00 0.00
> conf H
> ATOM 41 2H21 MOL 371 -8.669 -6.691 2.973 1.00 0.00
> conf H
> ATOM 42 C26 MOL 371 -9.001 -7.829 1.132 1.00 0.00
> conf C
> ATOM 43 C28 MOL 371 -7.520 -7.808 0.727 1.00 0.00
> conf C
> ATOM 44 1H28 MOL 371 -6.890 -7.910 1.641 1.00 0.00
> conf H
> ATOM 45 2H28 MOL 371 -7.257 -6.904 0.130 1.00 0.00
> conf H
> ATOM 46 3H28 MOL 371 -7.280 -8.579 -0.042 1.00 0.00
> conf H
> ATOM 47 C29 MOL 371 -9.870 -7.688 -0.128 1.00 0.00
> conf C
> ATOM 48 1H29 MOL 371 -9.704 -8.545 -0.822 1.00 0.00
> conf H
> ATOM 49 2H29 MOL 371 -9.502 -6.856 -0.772 1.00 0.00
> conf H
> ATOM 50 C30 MOL 371 -11.358 -7.519 0.181 1.00 0.00
> conf C
> ATOM 51 1H30 MOL 371 -11.944 -7.413 -0.762 1.00 0.00
> conf H
> ATOM 52 2H30 MOL 371 -11.789 -8.473 0.564 1.00 0.00
> conf H
> ATOM 53 C9 MOL 371 -11.111 2.006 5.223 1.00 0.00
> conf C
> ATOM 54 H91 MOL 371 -11.015 2.954 5.801 1.00 0.00
> conf H
> ATOM 55 H92 MOL 371 -11.883 2.072 4.421 1.00 0.00
> conf H
> ATOM 56 H93 MOL 371 -10.227 1.814 4.571 1.00 0.00
> conf H
> ATOM 57 C7 MOL 371 -12.629 1.237 7.021 1.00 0.00
> conf C
> ATOM 58 H71 MOL 371 -12.824 0.400 7.732 1.00 0.00
> conf H
> ATOM 59 H72 MOL 371 -13.509 1.486 6.383 1.00 0.00
> conf H
> ATOM 60 H73 MOL 371 -12.535 2.228 7.523 1.00 0.00
> conf H
> ATOM 61 O1 MOL 371 -9.981 1.799 8.008 1.00 0.00
> conf O
> ATOM 62 H7 MOL 371 -9.203 1.684 8.533 1.00 0.00
> conf H
> ATOM 63 O2 MOL 371 -8.900 -0.615 8.667 1.00 0.00
> conf O
> ATOM 64 H8 MOL 371 -8.521 -1.467 8.488 1.00 0.00
> conf H
> ATOM 65 C8 MOL 371 -12.693 -2.092 7.106 1.00 0.00
> conf C
> ATOM 66 H81 MOL 371 -12.768 -1.253 7.837 1.00 0.00
> conf H
> ATOM 67 H82 MOL 371 -12.658 -3.092 7.598 1.00 0.00
> conf H
> ATOM 68 H83 MOL 371 -13.633 -2.245 6.526 1.00 0.00
> conf H
> ATOM 69 C14 MOL 371 -13.471 -3.647 4.064 1.00 0.00
> conf C
> ATOM 70 1H14 MOL 371 -14.075 -3.084 4.813 1.00 0.00
> conf H
> ATOM 71 2H14 MOL 371 -13.353 -4.717 4.356 1.00 0.00
> conf H
> ATOM 72 3H14 MOL 371 -14.032 -3.789 3.111 1.00 0.00
> conf H
> ATOM 73 C23 MOL 371 -13.126 -6.587 1.564 1.00 0.00
> conf C
> ATOM 74 O4 MOL 371 -13.495 -7.063 2.589 1.00 0.00
> conf O
> ATOM 75 O3 MOL 371 -13.994 -6.269 0.602 1.00 0.00
> conf O
> ATOM 76 H25 MOL 371 -14.423 -5.458 0.857 1.00 0.00
> conf H
> ATOM 77 C27 MOL 371 -9.279 -9.157 1.857 1.00 0.00
> conf C
> ATOM 78 1H27 MOL 371 -10.354 -9.172 2.151 1.00 0.00
> conf H
> ATOM 79 2H27 MOL 371 -8.594 -9.328 2.720 1.00 0.00
> conf H
> ATOM 80 3H27 MOL 371 -8.985 -10.047 1.253 1.00 0.00
> conf H
> TER 81 MOL 371
>
> Sorry. I hope this time was good.
>
> Henar
>
>
>
>
>
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