[gmx-users] error occurred during simulation of HRAS protein (PDB ID: 3K8Y) in the presence of GTP, Calcium acetate, and crystal waters

[Dallas Warren]

The error message is informing you of what the issue is, pdb2gmx is
expecting the atom names within the coordinate file to match exactly what
is specified in the residue database (rtp)

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#atom-x-in-residue-yyy-not-found-in-rtp-entry

Your rtp entry shows that it expects the atoms to be named "C1 C2 H1 H2
..." and then your coordinate file shows they are actually named "C O OXT
..."

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sun, 23 Feb 2020 at 23:32, manindersingh rajawat <
rajawat.manindersingh at gmail.com> wrote:

> Dear all,
> I am trying to simulate *HRAS protein (PDB ID: 3K8Y)* in the presence of
> water in* GROMACS5.1.3* using *charmm36_nov2018 forcefield*. The protein
> has bound GTP analog GNP in the active site and calcium acetate in the
> allosteric site. I have changed the GNP to GTP. Separately saved PDB files
> of GTP, and protein (containing protein, calcium and acetate ions and
> crystal waters). Calcium and acetate ions of allosteric site and crystal
> waters were retained. Others ions were deleted. Calcium ion residue and
> atom was renamed as CAL ( original CA) and acetate residue as ACET
> (original ACT). Generated the topology parameters for GTP by swissparam.
> During simulation setup error occurred in the very first topology
> generation step.
> *command used:*
> gmx pdb2gmx -f receptor_water_calciumacetate.pdb -o processed.pdb -water
> spc -ignh
>
> *Fatal error:*
> *Atom C in residue ACET 0 was not found in rtp entry ACET with 7 atoms*
> *while sorting atoms.*
> Please suggest what to do next and how to rectify the above error. Or
> another way to setup this simulation.
> I have checked the merged.rtp file in charmm36 forcefield folder, it
> contains the following description for ACET:
> [ ACET ]
> [ atoms ]
> C1 CG331 -0.370 0
> C2 CG2O3 0.620 1
> H1 HGA3 0.090 2
> H2 HGA3 0.090 3
> H3 HGA3 0.090 4
> O1 OG2D2 -0.760 5
> O2 OG2D2 -0.760 6
> [ bonds ]
> C1 H1
> C1 H2
> C1 H3
> C1 C2
> C2 O1
> C2 O2
> [ impropers ]
> C2 O2 O1 C1
> Coordinates of calcium and acetate ion in the
> receptor_water_calciumacetate.pdb
> ATOM 1322 NE2 HIS A 166 -28.827 57.264 -83.683 1.00 33.20 N
> ATOM 1323 OXT HIS A 166 -34.901 59.235 -83.148 1.00 41.11 O
> *HETATM 1359 CAL CAL A 169 -24.508 52.328 -83.059 1.00 26.85 CA*
> *HETATM 1361 C ACET A 719 -24.066 52.359 -79.976 1.00 29.56 C *
> *HETATM 1362 O ACET A 719 -25.026 52.986 -80.477 1.00 29.41 O *
> *HETATM 1363 OXT ACET A 719 -23.241 51.869 -80.781 1.00 29.13 O *
> *HETATM 1364 CH3 ACET A 719 -23.910 52.206 -78.493 1.00 29.01 C*
> HETATM 1365 O HOH A 171 -0.065 68.481 -70.366 1.00 31.55 O
> HETATM 1366 O HOH A 172 -9.411 68.271 -67.530 1.00 15.88 O
> HETATM 1367 O HOH A 173 -13.003 66.200 -68.672 1.00 15.10 O
>
> Thanks,
> Maninder
>
>
> --
> Maninder Singh
> Research Fellow,
> LSN-104, Computational Biology and Bioinformatics Unit,
> Molecular and Structural Biology Division,
> CSIR-Central Drug Research Institute,
> Sector-10, Janakipuram Extension,
> Sitapur road,
> Lucknow
> India-226031
> M: +919129206276
> Email: rajawat.manindersingh at gmail.com
> --
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