Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber

From: Francesco Pietra <chiendarret.gmail.com>
Date: Thu, 30 Sep 2010 15:41:25 +0200

Your guess is probably quite correct

$AMBERHOME/exe/antechamber -i pha.NH3.pdb -fi pdb -o pha.mol2
-c bcc -s 2 -nc +1

pha.mol2 opens correctly with either Chimera or VMD and the
coordinates are the same as with pha.NH3.pdb. Here the input pdb file:

ATOM      1  N   PHA A   4      -1.444  -3.172   1.463  1.00  0.00           N
ATOM      2  CA  PHA A   4      -1.411  -3.377   2.909  1.00  0.00           C
ATOM      3  CB  PHA A   4      -0.430  -4.502   3.290  1.00  0.00           C
ATOM      4  CG  PHA A   4       0.978  -4.299   2.778  1.00  0.00           C
ATOM      5  CD1 PHA A   4       1.313  -4.654   1.460  1.00  0.00           C
ATOM      6  CD2 PHA A   4       1.983  -3.792   3.615  1.00  0.00           C
ATOM      7  CE1 PHA A   4       2.592  -4.399   0.959  1.00  0.00           C
ATOM      8  CE2 PHA A   4       3.269  -3.550   3.120  1.00  0.00           C
ATOM      9  CZ  PHA A   4       3.570  -3.837   1.784  1.00  0.00           C
ATOM     10  C   PHA A   4      -1.125  -2.032   3.569  1.00  0.00           C
ATOM     11  O   PHA A   4      -0.132  -1.783   4.209  1.00  0.00           O
ATOM     12  N2  PHA A   4      -2.043  -1.057   3.413  1.00  0.00           N
ATOM     13  H   PHA A   4      -0.644  -2.624   1.183  1.00  0.00           H
ATOM     14  HA  PHA A   4      -2.408  -3.690   3.220  1.00  0.00           H
ATOM     15  HB2 PHA A   4      -0.392  -4.568   4.377  1.00  0.00           H
ATOM     16  HB3 PHA A   4      -0.811  -5.445   2.897  1.00  0.00           H
ATOM     17  HD1 PHA A   4       0.576  -5.128   0.829  1.00  0.00           H
ATOM     18  HD2 PHA A   4       1.762  -3.586   4.652  1.00  0.00           H
ATOM     19  HE1 PHA A   4       2.825  -4.637  -0.068  1.00  0.00           H
ATOM     20  HE2 PHA A   4       4.029  -3.142   3.769  1.00  0.00           H
ATOM     21  HZ  PHA A   4       4.554  -3.625   1.392  1.00  0.00           H
ATOM     22  H21 PHA A   4      -2.882  -1.234   2.879  1.00  0.00           H
ATOM     23  H22 PHA A   4      -1.892  -0.150   3.830  1.00  0.00           H
ATOM     24  H1  PHA A   4      -1.419  -4.067   0.995  1.00  0.00           H
ATOM     25  H2  PHA A   4      -2.292  -2.684   1.211  1.00  0.00           H
CONECT   10    2   11   12
CONECT    2    3    1   10   14
CONECT    3    2    4   15   16
CONECT    5    4    7   17
CONECT    6    4    8   18
CONECT    7    5    9   19
CONECT    8    6    9   20
CONECT    4    3    5    6
CONECT    9    7    8   21
CONECT   13    1
CONECT   24    1
CONECT   25    1
CONECT   22   12
CONECT   23   12
CONECT   14    2
CONECT   15    3
CONECT   16    3
CONECT   17    5
CONECT   18    6
CONECT   19    7
CONECT   20    8
CONECT   21    9
CONECT    1    2   13   24   25
CONECT   12   10   22   23
CONECT   11   10
END
************

My task is preparing prmtop/inpcrd for a peptide containing
phenylalanine amide. This is why I tried to get prepin/frcmod files to
feed to leap along with the pdb file of the peptide. Could you please
suggest a promising move from here?
Thanks a lot
francesco pietra


On Thu, Sep 30, 2010 at 1:28 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Sep 30, 2010, Francesco Pietra wrote:
>
>> Incorrect handling of phenylalanine amide by antechamber 1.2 in amber
>> 10 (or mishandling of antechamber by the operator).
>>
>> Phenylalanine amide triprotonated at N, thus charge +1. The structure
>> is correct in both Chimera and VMD.
>>
>> $AMBERHOME/exe/antechamber -i pha.NH3.pdb -fi pdb -o pha.prepin -fo
>> prepi -c bcc -s 2 -nc +1
>>
>> $AMBERHOME/exe/parmchk -i pha.prepin -f prepi -o pha.frcmod
>>
>> These prepin and frcmod file are not accepted by Chimera, while VMD
>> shows a highly deformed structure (much too long C=O bond, phenyl
>> hydrogens out of plane and ring distorted; NH3 also distorted.
>>
>> Thanks for indicating my mistakes in the antechamber input files.
>
> Can you post the input pdb file so we can look at this?  There may be a
> problem in converting to internal coodinates.  As a check, try creating a mol2
> file rather than a prepin file: the output coordinates should be the same as
> the input ones.
>
> ....dac
>
>
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Received on Thu Sep 30 2010 - 07:00:10 PDT
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