[AMBER] Joining two files

From: Marco Malvaldi <marcoampelio.hotmail.com>
Date: Mon, 29 Oct 2012 11:47:35 +0100

Hello,I'm a new user of amber and I'm trying to simulate a non-biological object, namely a small organic molecule near a graphene slab.Trying to build up the system, I first build ,pdb, .prm and .crd the files for the two, together with the .frcmod files calculated by antechamber, and then try to join them. When i run leap with the script leap-join.in What I get is that atom types are not recognized (even if they are listed in .frcmod, and I load frcmod in the script). Before brutally use addPDBAtomListto get a one-by-one corresponcende, is there a smart way to make leap recognize the atom types?All files mentioned are in the .tgz archive attached.
Thanks in advance,Marco

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Received on Mon Oct 29 2012 - 04:00:03 PDT
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