On Sat, Jun 20, 2015 at 11:09 AM, Ramin Ekhteiari <ramin_ekh.yahoo.com>
wrote:
> Hi Dears,
> I am trying to generate parameter and topology files for my system using
> tleap module, but the system includes standard and non-standard residues
> while these residues have connected to each other.
> So I became confused how to do this.
> I tested following way:
> I discontented the non-standard residue from the system and generated
> parameter and topoloogy files using antechamber and then prepared following
> tleap script to combine standard and non-standard residues. (I removed H
> atoms form connection domains and defined bonds between standard and
> non-standard residues) But the result is not satisfied. A lot of topology
> and parameter error is appeared and the generated bonds are not displayed
> on the systems.
> I would be grateful for any advice.
>
​Have a look at tutorial B5 and A1 at
http://ambermd.org/tutorials/#ligands.
This shows you how to parametrize a covalent​ly bound custom residue. The
approach you're using below seems to be overly complicated and wlil most
likely result in non-physical, non-integer charges (since you're removing a
whole lot of hydrogen atoms and drawing in a lot of bonds).
HTH,
Jason
>
> set default PBradii mbondi2
> source leaprc.ff99SB
> source leaprc.gaff
>
> source leaprc.GLYCAM_06j-1
> loadamberprep UNK.prep
> loadamberparams UNK.frcmod
>
> m = loadpdb 4GA.pdb
>
> lig = loadpdb UNK-poly.pdb
>
>
> remove lig.8 lig.8.H11
> remove lig.9 lig.9.H11
> remove lig.10 lig.10.H11
> remove lig.11 lig.11.H11
> remove lig.12 lig.12.H11
> remove lig.13 lig.13.H11
> remove lig.14 lig.14.H11
>
> remove m.1 m.1.H6O
> remove m.2 m.2.H6O
> remove m.3 m.3.H6O
> remove m.4 m.4.H6O
> remove m.5 m.5.H6O
> remove m.6 m.6.H6O
> remove m.7 m.7.H6O
>
>
> bond lig.8.C1 m.1.O6bond lig.9.C1 m.2.O6
> bond lig.10.C1 m.3.O6
> bond lig.11.C1 m.4.O6
> bond lig.12.C1 m.5.O6
> bond lig.13.C1 m.6.O6
> bond lig.14.C1 m.7.O6
>
>
>
>
> COM = combine {m lig}
> saveamberparm COM test.prm7 test.rst7
> solvateBox TIP3PBOX 10.0
> saveamberparm COM test.wat.prm7 test.wat.rst7
> check m
> charge m
> quit
> Berk.
>
>
>
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jun 20 2015 - 10:00:03 PDT
