[gmx-users] Warning: atom is missing in residue

[Justin Lemkul]

On 2/14/14, 6:24 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> When I run gromacs, there is an issue with the molecules with more than one residue. for example, for this pdb file:
>
> ATOM      1  C1  VOD     0       8.441   1.158   0.141  1.00  0.00           C
> ATOM      2  H1  VOD     0       9.420   1.340   0.570  1.00  0.00           H
> ATOM      3  H2  VOD     0       8.580   0.090   0.040  1.00  0.00           H
> ATOM      4  H3  VOD     0       8.696   0.757  -0.666  1.00  0.00           H
> ATOM      5  C2  VOD     1       7.270   1.800   0.740  1.00  0.00           C
> ATOM      6  H4  VOD     1       6.440   1.830   0.030  1.00  0.00           H
> ATOM      7  H5  VOD     1       6.950   1.150   1.550  1.00  0.00           H
> ATOM      8  O   VOD     1       7.640   3.100   1.130  1.00  0.00           O
> ATOM      9  H6  VOD     1       8.300   3.360   0.500  1.00  0.00           H
>
> The corresponding residue in aminoacids.rtp is:
>
> [ VOD ]
>   [ atoms ]
>     C1  CH2    -0.18000     0
>     H1    H     0.06000     0
>     H2    H     0.06000     0
>     H3    H     0.06000     0
>     C2  CH3     0.14500     1
>     H4    H     0.06000     1
>     H5    H     0.06000     1
>      O   OA    -0.68300     1
>     H6    H     0.41800     1
>   [ bonds ]
>     C1   H1    gb_2
>     C1   H2    gb_2
>     C1   H3    gb_2
>     C1   C2    gb_27
>     C2   H4    gb_2
>     C2   H5    gb_2
>     C2   O     gb_18
>      O   H6    gb_1
>   [ angles ]
> ;  ai    aj    ak   gromos type
>      H1    C1    H2     ga_19
>      H1    C1    H3     ga_19
>      H1    C1    C2     ga_19
>      H2    C1    H3     ga_19
>      H2    C1    C2     ga_19
>      H3    C1    C2     ga_19
>      C1    C2    H4     ga_19
>      C1    C2    H5     ga_19
>      C1    C2     O     ga_13
>      H4    C2    H5     ga_19
>      H4    C2     O     ga_30
>      H5    C2     O     ga_30
>      C2     O    H6     ga_30
>
> Problem: When I use pdb2gmx here are the warnings:
>
> -----------------------------------
>
> WARNING: atom C2 is missing in residue VOD 0 in the pdb file
>
>
> WARNING: atom H4 is missing in residue VOD 0 in the pdb file
>
>
>
> WARNING: atom H5 is missing in residue VOD 0 in the pdb file
>
>
> WARNING: atom O is missing in residue VOD 0 in the pdb file
>
>
> WARNING: atom H6 is missing in residue VOD 0 in the pdb file
> -----------------------
>
> When I combine these 2 residues and make it one, there is no warning. Does anybody know what is the problem?
>

Each .rtp entry is a residue.  Your coordinate file splits one residue defined 
in the .rtp file into two different residues, neither of which matches the .rtp 
definition, thus pdb2gmx fails.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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