[gmx-users] Fatal error pdb

[Justin Lemkul]

On 9/7/15 2:00 PM, Poncho Arvayo Zatarain wrote:
> Hello: I'm trying to simulate an halothane molecule in water. I download the halothane at pubchem and converted to pdb format using
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> 	open babel 2.3.2 but when i use pdb2gmx and select OPLS/AA forcefield it appears: Fatal error: halothane.pdb. Could you help me please? is there any problem with my pdb?. This is my pdb format:
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Have you created a suitable .rtp entry for halothane?  I doubt it exists already 
in pdb2gmx, which cannot magically create a topology for anything.  I guarantee 
that "LIG" will trigger a different fatal error.

Please copy and paste errors exactly, otherwise it is pointless to try to guess 
what is going on.  Your error (if it is what I think it is) suggests that the 
file simply doesn't exist.

-Justin

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> COMPND    3562
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> AUTHOR    GENERATED BY OPEN BABEL 2.3.2
> HETATM    1 BR   LIG     1       1.825  -1.412 -0.043  1.00  0.00          Br
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> HETATM    2 CL   LIG     1       1.493   1.601 -0.049  1.00  0.00          Cl
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> HETATM    3  F   LIG     1      -1.442   0.983  0.438  1.00  0.00           F
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> HETATM    4  F   LIG     1      -0.715  -0.052 -1.340  1.00  0.00           F
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> HETATM    5  F   LIG     1      -1.239  -1.182  0.454  1.00  0.00           F
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> HETATM    6  C   LIG     1      -0.666  -0.040  0.010  1.00  0.00           C
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> HETATM    7  C   LIG     1       0.744   0.102  0.530  1.00  0.00           C
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> HETATM    8  H   LIG     1       0.765   0.103  1.623  1.00  0.00           H
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> CONECT    1    7
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> CONECT    2    7
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> CONECT    3    6
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> CONECT    4    6
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> CONECT    5    6
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> CONECT    6    3    4    5    7
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> CONECT    6
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> CONECT    7    1    2    6    8
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> CONECT    7
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> CONECT    8    7
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> MASTER        0    0    0    0    0    0    0   0    8    0    8    0
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> END
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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