Hello everyone!!
I generated the topology of my heteromolecule by ATB server using Semi emperical method. I want to run a simulation using gromacs using gromos96 53a6 force field and tip3p water model. The gromp_mpi command is throwing the error atomtype HS14 not found.
Please suggest How to proceed.
Thanks
Details on non-official GROMOS atom types used by the ATB are available here: https://atb.uq.edu.au/index.py?tab=faq.
The HS14 is used for polar hydrogen atoms when there is an atom of opposite charge in the 1-4 position. In such cases the fact that polar hydrogen atoms do not have any Lennard Jones terms can cause simulations to crash (e.g. constraint algorithm failure). Updated versions of the GROMACS parameter files are available from the ATB site which contain all the additional Lennard Jones parameters that the ATB uses.
Changing the HS14 to H in the itp file is a fine solution, provided the charge difference on the hydrogen and it's 1-4 neighbour is not high enough to cause distorted geometry or simulation failure. Changing HS14 to HC would not be advised as this will effect all non-bonded interactions involving the hydrogen atom and cause significant inaccuracies particularly in the case of hydrogen bonding.
I have downloaded topology file in 53a6 ff gromacs format united atom and the topology file contains this HS14 assigned to the atom H6, H7, H16, H17.
I went through the paper of 53a6 and in that, the atom type for all hydrogen bonded to non carbon is H. So, should I replace HS14 by H and proceed as all the HS14 type atom is actually bonded to oxygen in the from of -OH. Please suggest me on this!!!!!!
One more thing Which I would like to discuss is that the atom type for carbon bound in ring, sp2, sp3 are different as defined in the original paper and I have also verified it by looking into protein topology file generated by gromacs. But the topology generated by ATB server has assigned atom type C to all the carbon atom (even to the carbon preset in ring) which stands for bare carbon. So, Knowing these contradictions, should I proceed ahead or not. How to rectify this issue? please suggest!!!!!!!!
Thank you
Dear Kumar
HS14 atom type doesn;t exist in 53a6 topology base, but you can change it manually for example to the HC or H. During the simulation system communicate with bonded and nonbonded topology base then it finds appropriate atom type.
Details on non-official GROMOS atom types used by the ATB are available here: https://atb.uq.edu.au/index.py?tab=faq.
The HS14 is used for polar hydrogen atoms when there is an atom of opposite charge in the 1-4 position. In such cases the fact that polar hydrogen atoms do not have any Lennard Jones terms can cause simulations to crash (e.g. constraint algorithm failure). Updated versions of the GROMACS parameter files are available from the ATB site which contain all the additional Lennard Jones parameters that the ATB uses.
Changing the HS14 to H in the itp file is a fine solution, provided the charge difference on the hydrogen and it's 1-4 neighbour is not high enough to cause distorted geometry or simulation failure. Changing HS14 to HC would not be advised as this will effect all non-bonded interactions involving the hydrogen atom and cause significant inaccuracies particularly in the case of hydrogen bonding.
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