Re: [AMBER] Fw: covalent molecule and modified residue parameters

From: Sarah Jane <>
Date: Mon, 7 Sep 2020 11:20:19 +0000 (UTC)

 Hi Dac,
I edited mol2 file and uploaded like mentioned in 'help loadMol2'.
I tried 'desc' command and attached leap.log file.
Please advice.
Thanks,Sarah On Thursday, 3 September 2020, 21:29:20 BST, David A Case <> wrote:
 On Thu, Sep 03, 2020, Sarah Jane wrote:
>  > loadmol2 HAR.mol2
      Loading Mol2 file: ./HAR.mol2
      Reading MOLECULE named UNK

Look at the second line of your HAR.mol2 file: it says the the name of
the unit is "UNK".  See if changing that to "HAR" helps.

Note that if you type "help loadMol2" in tleap, it gives a different
syntax than the one you use above.  I'd suggest following the help

>  seq = sequence {ACE HAR NHE}
>  Error: sequence: Illegal UNIT named: HAR

Before you do this, use the "desc" command to see what is in the HAR

...good luck....dac

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Received on Mon Sep 07 2020 - 04:30:02 PDT
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