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Atom -C not found in residue SER 11, rtp entry SER while adding hydrogens. My protein chain starts from SER 11. I am continuously facing this error. Can anyone help me out with this?
Please copy and paste the full screen output from pdb2gmx.
Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
This error I am facing when Proline was the first amino acid residue of the protein chain.
That’s a different issue than what you first posted and we still need the full terminal output from the command you ran (including the command).
Okay I am mentioning in detail. I have a protein with a single chain. There is a phosphorylation in tyrosine 129. It a complete structure starting from Methionine (residue 1). Now i am running pdb2gmx command as: gmx pdb2gmx -ignh -f UENpdbreader.pdb -o UENpdbreader_processed.gro
I have downloaded Charmm 36 ff.tar file from Mackerell lab site. I chose charm36 ff and tip3p (charmm modified) water model. Now I am getting this error continuously:
Fatal error:
Atom -C not found in residue MET 1, rtp entry MET while adding hydrogens.
Answered here: Newest CHARMM36 port for GROMACS - #11 by jalemkul
Thank you so much. Do we need to download this toppar_c36_jul2022.tgz?
I have downloaded the updated toppar file which has the aminoacid.rtf file updated. I am getting this new awkward error: Opening force field file ./charmm36-jul2022.ff/aminoacid1.rtp
Warning: file does not end with a newline, last line:
��ࡱ▒�
There should be no file called aminoacid1.rtp in the directory, so that is something perhaps you have inadvertently created. Never open any GROMACS force field, database, etc. file with anything other than a plain-text editor. If you have, delete those files and start over.
Sir, I could do the pdb2gmx step and have generated the .gro and topology files. I have completed till solvation step. Now I am facing an issue in the gmx grompp step. I am giving the command and the whole output here.
sahalab-uac-l@sahalab-uac-l-Vostro-3710:~/Documents/Ligand$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2021.4-Ubuntu-2021.4-2 (-:
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GROMACS: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/sahalab-uac-l/Documents/Ligand
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
WARNING 1 [file ions.mdp, line 32]:
Unknown left-hand ‘integrator’ in parameter file
Setting the LD random seed to 2075651327
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_P’
turning all bonds into constraints…
NOTE 1 [file topol.top, line 74240]:
System has non-zero total charge: -19.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.
WARNING 2 [file topol.top, line 74240]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------
NOTE 2 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 681)
Fatal error:
number of coordinates in coordinate file (solv.gro, 198459)
does not match topology (topol.top, 7867)