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
