[AMBER] problem in tleap with head and tail atom assignment

From: Cramariuc Oana <oana.cramariuc.tut.fi>
Date: Wed, 18 Apr 2012 20:10:34 +0000

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 Wed Apr 18 2012 - 13:30:04 PDT
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