Dear Amber users,
I have been trying to use AMBER to perform a residue perturbation using the TI code. As far as I understand, if one is working with e.g. a tripeptide such as (using one-letter amino acid codes) PTG and wants to perturb it to PYG, the correct way to do it in AMBER is to generate a composite residue (which we will call MUT), which results in P-MUT-G, where MUT contains atoms from both T and Y. Then one sets the TI masks to be all the corresponding atoms from the MUT residue, and the SC masks define the dummy atoms as usual.
However, if I try to do that with a very simple test input of this tripeptide in vacuum, I get NaNs in the non-1-4 electrostatic part of the calculation. However, the van der Waals interactions are finite, which means that the problem is not a clash. Even more strangely, if one sets all charges to 0, the NaNs are still there, which is completely unexpected. On the other hand, if one removes the periodic boundary conditions (i.e. set ntb=0), the simulation runs fine, indicating that these infinities stem from the PME part of the code.
I am attaching an input parm7, rst7 and mdin file which reproduce the error. Does anyone have any clue as to what might be going wrong? Any help would be much appreciated.
Kind regards,
Miro
Miroslav Suruzhon MSc PhD
Molecular Dynamics Research Scientist
+44 (0) 7719 025700
Exscientia
The Schrödinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE
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Received on Tue Oct 04 2022 - 07:30:02 PDT
