I have tried to run simulation for protein complex of NRAS(5UHV) bound with Mg and GTP.
However I have encountered the following error while using pdb2gmx:
Program pdb2gmx, VERSION 4.6.7
Source code file: /home/nithyanan/Bioinformatics/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1148
Fatal error:
atom N not found in buiding block 2GTP while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I have gone through the .rtp file and .tdb file but could'nt really understand the error.
I used charmm36-mac2019 ff.
Can someone please explain to me clearly what I should do to rectify this error.
I have uploaded the pdb file I used for reference.
i don't use Gromacs but could it be that Gromacs assumes the GTP molecule is an amino acid residue?
Hi Nithyanan,
I would better recommend you using Amber to study these types of systems.
https://ambermd.org/tutorials/
http://research.bmh.manchester.ac.uk/bryce/amber/
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