Thank you all for helping! It's fine now.
regards, Oana
________________________________________
From: FyD [fyd.q4md-forcefieldtools.org]
Sent: 19 April 2012 13:14
To: AMBER Mailing List
Subject: Re: [AMBER] problem in tleap with head and tail atom assignment
Dear Oana Cramariuc,
You can find examples for head/tail & connect0/connect1 in R.E.DD.B.
and information in tutorials . q4md-forcefieldtools.org
See for instance:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
Examples:
central fragment
http://q4md-forcefieldtools.org/REDDB/projects/F-86/
http://q4md-forcefieldtools.org/REDDB/projects/F-86/script1.ff
slighly more complex:
http://q4md-forcefieldtools.org/REDDB/projects/F-81/
http://q4md-forcefieldtools.org/REDDB/projects/F-81/script1.ff
regards, Francois
Quoting Cramariuc Oana <oana.cramariuc.tut.fi>:
> Dear all,
>
>
> I have created a nonstandard HID residue which I have named HIL. My
> tleap input for producing the .lib and .prmtop file from a mol2 file
> (with correct atom types and charges) and from the .frcmod file is
> the following:
>
> source leaprc.ff99SB
> source leaprc.gaff
> HIL = loadmol2 HIL.mol2
> loadamberparams HIL.frcmod
> set HIL head HIL.1.N
> set HIL tail HIL.1.C
> set restype protein
> set name HIL
> saveoff HIL hil.lib
> saveamberparm HIL hil.prmtop hil.inpcrd
>
> The problem is that when constructing the whole protein, the HIL
> residue does not connect to the adjacent ones.
>
> By comparing the .lib file for my non-standard residue with the .lib
> file of HID in $AMBERHOME, I realized that the difference is in the:
>
> !entry.HIL.unit.residueconnect table int c1x int .... I have: 0 0
> 0 0 0 0 instead of 1 16 0 0 0 0
>
> The rest of the fields are correct, including the field:
> !entry.HIL.unit.connect array int
> where I also have correctly the atom head 1 and atom tail 16.
>
> If I edit by hand the missing numbers then I get a correct protein
> structure with linked residues.
>
> My question is if there is something that I do wrong when
> constructing the lib or is there a bug in the program?
>
> Thank you for your help,
> Oana Cramariuc
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Received on Thu Apr 19 2012 - 05:00:03 PDT
