Hi,
Have you checked to make sure they're not in the same chain, ie your
receptor and ligand are separated out as chain A, B, C?
The other thing that's an easy try is to see if it works when you load/make
them one at a time with a new tleap session each time.
Best,
Kenneth
On Mon, Jan 25, 2021 at 8:46 PM Devlina Chakravarty <
devlina.chakravarty.gmail.com> wrote:
> Hi,
>
> I need to perform MMPBSA analysis on a protein complex, I only have the
> trajectory in a PDB format (as in models 1 to N depicting frames of the
> simulation). To run MMPBSA I need to generate topology files for the
> complex, the receptor, and ligand separately, as well as the trajectory
> file following the tutorial on Ras-Raf complex from Amber (
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm)
>
> For the first step I generated the AMBER .crd trajectory using the first
> model/frame from the PDB trajectory as a parameter file and the following
> CPPTRAJ commands:
> """
>
> parm top_model.pdb
>
> trajin 6vw1-0-trj_25ns_transMD1.pdb 1 last 40
>
> autoimage
>
> rms first mass .CA
>
> trajout 6vw1_nat_md1.crd nobox
>
> go
>
> quit
>
>
> """
>
>
> Then, I have leap to generate topology files for the complex, receptor, and
> the ligand
>
> """
>
> source leaprc.protein.ff14SB
>
> loadamberparams gaff.dat
>
> a = loadPdb top_model.pdb
>
> check a
>
> set default PBRadii mbondi2
>
> saveAmberParm a 6vw1_nat1.top 6vw1_nat1.crd
>
> savepdb a 6vw1-leap.pdb
>
> b = loadPdb top_model1_A.pdb
>
> saveAmberParm b 6vw1_nat1_A.top 6vw1_nat1_A.crd
>
> c = loadPdb top_model1_B.pdb
>
> saveAmberParm c 6vw1_nat1_B.top 6vw1_nat1_B.crd
>
> quit
>
>
> """
>
>
> The problem is when I tried to visualize the .top and .crd file on VMD,
> there are strange artifacts and connections that shouldn't be there, like
> the first residue of the second chain is connected to the last residue to
> the first chain (although the PDB file used to generate the topology file
> has TER in between the two chains). I have removed all HETATMs and hydrogen
> atoms from the PDB files before using them in leap and cpptraj. I have also
> renumbered the residues to make them continuous starting from 1. I am not
> sure how to fix this issue, where am I going wrong. Any help will be
> greatly appreciated,
>
> Thank you,
> Devlina
>
> --
> Devlina Chakravarty
> Postdoctoral Associate
> Department of Chemistry
> Rutgers University - Camden
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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here could not dream of heaven?
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Received on Tue Jan 26 2021 - 12:00:02 PST
