Re: [AMBER] Bug in tleap savemol2?

From: David Minh <dminh.iit.edu>
Date: Wed, 23 Jul 2014 15:05:22 -0500

>
> On Jul 23, 2014, at 9:41 AM, David Minh <dminh.iit.edu> wrote:
>
>> Hi all,
>>
>> I?m trying to set up a ?pipeline? that uses pdb2pqr to set receptor protonation states and then AmberTools to prepare prmtop and mol2 files. The mol2 files will be used in UCSF DOCK. I am using the following script in tleap:
>>
>> source leaprc.ff14SB
>> set default PBRadii bondi
>>
>> # Receptor
>> protein = loadpdb 3cqwA.0.amber.pqr
>> saveamberparm protein 3cqwA.0.prmtop 3cqwA.0.inpcrd
>> savepdb protein 3cqwA.0.amber.pdb
>> savemol2 protein 3cqwA.0.mol2 0 # default atom types, seems to have a bug
>> quit
>>
>> This successfully generates prmtop, inpcrd, and pdb files. However, tleap crashes at the end of this script:
>>
>> ...
>> Writing pdb file: 3cqwA.0.amber.pdb
>> Converting N-terminal residue name to PDB format: NARG -> ARG
>> Converting C-terminal residue name to PDB format: CTHR -> THR
>> Writing mol2 file: 3cqwA.0.mol2
>> /Users/dminh/Installers/amber14/bin/tleap: line 17: 1183 Abort trap: 6 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
>>
>> There is no further information in leap.log. Any ideas or suggestions?
>
> Maybe the PQR file doesn't adhere to the PDB standard enough. Keep in mind that PQR files are whitespace-delimited, whereas PDB files are not. They were designed to be very similar, but it's possible the PDB parser isn't handling your PQR quite right.
>
> I would suggest converting your PQR file to a PDB file and using that. If that still doesn't work, you can post your input structure here and someone can take a look at it.
>
> As a workaround, you can use ambpdb or cpptraj to write a mol2 file from your prmtop.
>
> HTH,
> Jason


Thanks for the suggestion, Jason! I was able to get around the issue with ambpdb. However, it still might be worth looking into why tleap fails in this case.

I donít think the issue was following the PDB standard, because tleap seems to have read the file without any issues. The main difference between the original PQR and a standard PDB file (as output from tleap) was the width of the occupancy and beta columns. Below, I shrunk this width and kept only the first two residues:

ATOM 1 N ARG 1 3.588 3.574 -6.586 0.13 1.82
ATOM 2 CA ARG 1 3.640 4.526 -7.716 0.02 1.90
ATOM 3 C ARG 1 4.499 5.693 -7.362 0.72 1.90
ATOM 4 O ARG 1 4.635 6.632 -8.144 0.60 1.66
ATOM 5 CB ARG 1 2.218 5.025 -8.017 0.01 1.90
ATOM 6 CG ARG 1 1.553 5.722 -6.828 0.02 1.90
ATOM 7 CD ARG 1 0.051 5.942 -7.012 0.09 1.90
ATOM 8 NE ARG 1 -0.611 4.615 -6.864 0.56 1.82
ATOM 9 CZ ARG 1 -1.953 4.490 -7.078 0.82 1.90
ATOM 10 NH1 ARG 1 -2.692 5.579 -7.437 0.86 1.82
ATOM 11 NH2 ARG 1 -2.556 3.273 -6.933 0.86 1.82
ATOM 12 HA ARG 1 4.029 4.044 -8.508 0.12 1.10
ATOM 13 HE ARG 1 -0.088 3.840 -6.615 0.35 0.60
ATOM 14 HG2 ARG 1 1.685 5.167 -6.003 0.03 1.48
ATOM 15 HG3 ARG 1 1.981 6.619 -6.689 0.03 1.48
ATOM 16 HH22 ARG 1 -3.515 3.201 -7.070 0.44 0.60
ATOM 17 HH21 ARG 1 -1.993 2.489 -6.691 0.44 0.60
ATOM 18 H1 ARG 1 2.881 3.861 -5.941 0.20 0.60
ATOM 19 HD3 ARG 1 -0.106 6.276 -7.913 0.05 1.38
ATOM 20 HD2 ARG 1 -0.266 6.535 -6.308 0.05 1.38
ATOM 21 H2 ARG 1 3.375 2.661 -6.930 0.20 0.60
ATOM 22 H3 ARG 1 4.473 3.557 -6.124 0.20 0.60
ATOM 23 HH12 ARG 1 -3.663 5.459 -7.566 0.44 0.60
ATOM 24 HH11 ARG 1 -2.243 6.449 -7.559 0.44 0.60
ATOM 25 HB3 ARG 1 1.660 4.244 -8.265 0.02 1.48
ATOM 26 HB2 ARG 1 2.268 5.674 -8.764 0.02 1.48
ATOM 27 N VAL 2 5.134 5.643 -6.175 0.41 1.82
ATOM 28 CA VAL 2 5.911 6.766 -5.747 0.08 1.90
ATOM 29 C VAL 2 7.361 6.392 -5.793 0.59 1.90
ATOM 30 O VAL 2 7.752 5.276 -5.456 0.56 1.66
ATOM 31 CB VAL 2 5.565 7.199 -4.345 0.29 1.90
ATOM 32 CG1 VAL 2 6.193 6.211 -3.357 0.31 1.90
ATOM 33 CG2 VAL 2 5.978 8.659 -4.118 0.31 1.90
ATOM 34 HA VAL 2 5.761 7.523 -6.389 0.09 1.38
ATOM 35 HG11 VAL 2 6.812 6.703 -2.748 0.07 1.48
ATOM 36 HG21 VAL 2 5.606 8.969 -3.246 0.07 1.48
ATOM 37 HB VAL 2 4.584 7.130 -4.223 0.02 1.48
ATOM 38 HG12 VAL 2 5.471 5.776 -2.823 0.07 1.48
ATOM 39 HG13 VAL 2 6.701 5.517 -3.864 0.07 1.48
ATOM 40 H VAL 2 5.005 4.770 -5.653 0.27 0.60
ATOM 41 HG23 VAL 2 6.974 8.715 -4.103 0.07 1.48
ATOM 42 HG22 VAL 2 5.616 9.217 -4.861 0.07 1.48

and still the same error occurs.
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Received on Wed Jul 23 2014 - 13:30:02 PDT
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