[AMBER] Issue with addAtomType: Syntax Error

From: Korey M Reid <koreyr.unr.edu>
Date: Thu, 17 Nov 2016 20:14:36 +0000

Hello all,

I am running into a problem when importing my pdb file containing a heme such as myoglobin (in my case HbI - 4sdh) using amber16 with ambertools16. I have preprocessed my pdb for amber input, I used the united atom ff from http://archive.ambermd.org/201012/att-0192/ .<http://research.bmh.manchester.ac.uk/bryce/amber.> I first converted the docs from dos2unix fixing an error addressed here: http://archive.ambermd.org/201403/0273.html . Now I am left with undefined atom types for the heme prosthetic group (file attached to message leap_*.log). I have tried to addAtomTypes within tleap but as can be seen in the file I get a syntax error (in the file it shows only:
>addAtomType { { "FE" "FE" "sp2" } }

I have tried several variations for the type name including Fe2+, Fe2, Fe and all permutations of lower and upper case (not shown in representative file).

What is the procedure for running this command? Is there a texbook way of adding this to the frcmod.hemall file or the heme_all.in file so that when the files are loaded the types are added (to mirror what is seen in the leaprc files)?

Thank you for your help!!!

Best Wishes,
Korey Reid

ps I attached all files relating to this issue.

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Received on Thu Nov 17 2016 - 12:30:02 PST
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