[gmx-users] Halothane rtp and pdb file

[Justin Lemkul]

On 9/19/15 5:40 PM, Poncho Arvayo Zatarain wrote:
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>
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> Hello, i want to run a simulation of halothane in a DPPC membrane. I have the pdb file of halothane and run the pdb2gmx (pdb2gmx -f halotano.pdb -o halotano.gro -water spc) with GROMOS 53a6 forcefield and the rtp file. The output marks this: Warning starting residue i825, 1493, -1442, -01715, -1239 in chain not identified as protein, DNA, RNA. Fatal error: Residue 1 not found in residue topology database. How can i solve this error? I think it could be a trouble with rtp or pdb file. I attached it. This is my rtp file
>
> bondedtypes ]
> ; bonds  angles  dihedrals  impropers
>      7
>
> [ HLT ]
>
>   [ atoms ]
> ; name  type  charge  chargegroup
>     C1     C    0.66
>     F1     F   -0.22
>     F2     F   -0.22
>     F3     F   -0.22
>     C2     C    0.215
>     Br     Br  -0.16
>     Cl     Cl  -0.18
>     H      H    0.125
>
>   [ bonds ]
> ;atom1 atom2      b0      kb
>       C2    H
>       C1    F1
>       C1    F2
>       C1    F3
>       C2    Cl
>       C2    Br
>       C1    C2
>
>   [ exclusions ]
> ;atom1 atom2
>
>   [ angles ]
> ;atom1 atom2 atom3    th0    cth
>
>   [ dihedrals ]
> ;atom1 atom2 atom3 atom4   phi0     cp   mult
>
>   [ impropers ]
> ;atom1 atom2 atom3 atom4     q0     cq
>

IIRC by specifying empty directives, no interactions are written.  Certainly 
there are at least angles that you want.

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> And this is my halothane pdb file that i converted using OPEN BABEL 2.2
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> COMPND    3562
>
> AUTHOR    GENERATED BY OPEN BABEL 2.3.2
> HETATM    1 BR  1   1.825  -1.412  -0.043  1.00
> 0.00
>
> HETATM    2 CL  1   1.493   1.601  -0.049  1.00
> 0.00
>
> HETATM    3  F  1  -1.442   0.983   0.438  1.00
> 0.00
>
> HETATM    4  F  1  -0.715  -0.052  -1.340  1.00
> 0.00
>
> HETATM    5  F  1  -1.239  -1.182   0.454  1.00
> 0.00
>
> HETATM    6  C  1  -0.666  -0.040   0.010  1.00
> 0.00
>
> HETATM    7  C  1   0.744   0.102   0.530  1.00
> 0.00
>
> HETATM    8  H  1   0.765   0.103   1.623  1.00
> 0.00
>

You have non-unique atom names.  The coordinate file must match the .rtp file.

-Justin

-- 
==================================================

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

==================================================