[gmx-users] Errors pdb2gmx

[Justin Lemkul]

On 11/30/15 7:53 AM, Stefania Evoli wrote:
> Hi everybody,
>
> I’m simulating for the first time the riboswitch in presence of metals,
> usually I work only with proteins. I modified the pdb file to have the 5’ and
> 3’ terminals but when I try to use pdb2gmx_mpi_d (Gromacs 5.0.5) to generate
> gro and top file with the ff amber99sb-ildn I get the error 'Residue 'F' not
> found in residue topology database’. I checked in the atomtype database
> fluorine is called with ‘F’. I don’t understand what I’m doing wrong. Could
> someone help me, please?
>

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Only OPLS-AA supports F- anions.  What is relevant is the content of the *.rtp 
files.  The F atom type can refer to an anionic or non-ionized form (generally 
the latter).

If the ion is just part of some crystallized salt, it may be functionally 
irrelevant and can be removed.  That's for you to decide based on what you know 
about your structure.

-Justin

> The last part of my pdb file is like
>
>
> ATOM   1109  N1    G A  52       5.885  15.987 -29.904  1.00106.05
> N
>
> ATOM   1110  C2    G A  52       6.739  16.703 -29.104  1.00108.63
> C
>
> ATOM   1111  N2    G A  52       7.547  17.572 -29.727  1.00108.84
> N
>
> ATOM   1112  N3    G A  52       6.796  16.580 -27.788  1.00112.10
> N
>
> ATOM   1113  C4    G A  52       5.924  15.660 -27.307  1.00113.15
> C
>
> TER    1114        G A  52
>
> HETATM 1115 MG    MG A 101     -12.105  14.253 -12.775  1.00 42.94
> MG
>
> HETATM 1116 MG    MG A 102      -1.621  16.836 -16.694  1.00 57.68
> MG
>
> HETATM 1117 MG    MG A 103     -10.729  16.277 -10.240  1.00 54.29
> MG
>
> HETATM 1118 MG    MG A 104     -13.066  14.112 -10.060  1.00 38.13
> MG
>
> HETATM 1119 MG    MG A 105      10.592  16.076 -23.407  1.00114.31
> MG
>
> HETATM 1120  F     F A 106     -11.635  14.767 -10.999  1.00 37.49
> F
>
> HETATM 1121  K     K A 107     -15.304  15.848 -12.170  1.00 75.41
> K
>
> HETATM 1122  O   HOH A 201      -3.046  15.371 -17.019  1.00 60.47
> O
>
> HETATM 1123  O   HOH A 202      -9.781  18.114  -9.629  1.00 39.40
> O
>
> HETATM 1124  O   HOH A 203     -10.387  15.232 -13.471  1.00 40.03
> O
>
> HETATM 1125  O   HOH A 204     -13.816  13.609 -11.929  1.00 36.59
> O
>
> HETATM 1126  O   HOH A 205     -11.326  12.355 -12.487  1.00 41.22
> O
>
> HETATM 1127  O   HOH A 206     -16.414  13.856 -13.423  1.00 46.60
> O
>
> HETATM 1128  O   HOH A 207     -14.624  13.020  -9.235  1.00 48.49
> O
>
> HETATM 1129  O   HOH A 208     -12.325  12.095 -10.081  1.00 42.16
> O
>
> HETATM 1130  O   HOH A 209      -2.988  18.280 -16.047  1.00 46.13
> O
>
> HETATM 1131  O   HOH A 210      -0.566  15.325 -17.495  1.00 50.52
> O
>
> HETATM 1132  O   HOH A 211      -1.864  17.062 -18.764  1.00 53.50
> O
>
> HETATM 1133  O   HOH A 212      -7.387  18.633 -10.494  1.00 40.88
> O
>
> HETATM 1134  O   HOH A 213     -10.571   9.493 -10.828  1.00 52.53
> O
>
> HETATM 1135  O   HOH A 214      -3.704  27.050  -9.237  1.00 60.38
> O
>
> HETATM 1136  O   HOH A 215     -11.800  42.303 -11.267  1.00 59.89
> O
>
> HETATM 1137  O   HOH A 216     -10.633  32.221 -20.335  1.00 79.49
> O
>
> HETATM 1138  O   HOH A 217      -0.062   4.774  -3.205  1.00 88.09
> O
>
> HETATM 1139  O   HOH A 218     -25.127  -9.600   1.612  1.00 71.27
> O
>
> HETATM 1140  O   HOH A 219     -16.317  25.773  -3.277  1.00 85.21
> O
>
> HETATM 1141  O   HOH A 220     -19.507  19.430  -0.328  1.00 87.20
> O
>
> HETATM 1142  O   HOH A 221     -33.017  10.031  -0.836  1.00 72.84
> O
>
>
> I also tried to use ‘TER’ at the end of each ion (in previous Gromacs version
> it worked) but I didn’t solve the problem.
>
> Thank you,
>
> Stefania
>
>
> — Dr. Stefania Evoli Post-Doctoral Fellow King Abdullah University of Science
> and Technology Catalysis center - Bldg. 3, 4th floor, 4231–WS18 Thuwal,
> Kingdom of Saudi Arabia stefania.evoli at kaust.edu.sa
>
>
>
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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

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