I think you have to explicitly set the connect0 and connect1 by hand. In
any case, it seems like it's working now for you, and that's the
appropriate change to make in your .lib file.
HTH,
Jason
On Wed, Apr 18, 2012 at 4:10 PM, Cramariuc Oana <oana.cramariuc.tut.fi>wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 18 2012 - 14:30:03 PDT
