Re: [AMBER] how to add lipid

From: mohammad r <>
Date: Mon, 24 Aug 2015 17:28:48 +0000 (UTC)

I tried loadpdb, but it couldnot read it.

     On Monday, August 24, 2015 9:23 PM, mohammad r <> wrote:

 Thank you very much Bill;I've generated the initial structure of my system but tleap cannot read it. I don't know how to convert it to amber format.

     On Monday, August 24, 2015 11:37 AM, mohammad r <> wrote:

 Thanks you Bill;
So I'm gona first generating the coordinate file of DOPC then by using packmol try to add it to my water-peptide system.

     On Monday, August 24, 2015 10:45 AM, Bill Ross <> wrote:

 Hi Mohammad,

Read the instructions for the loadpdb command in leap.

> dopc = loadpdb dopc.pdb

Then try saveamberparm and see what parameters you need.


<div>-------- Original message --------</div><div>From: mohammad r <> </div><div>Date:08/23/2015  9:38 PM  (GMT-08:00) </div><div>To: AMBER Mailing List <> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
</div>Thank you Bill;
You mean that I should first build the lipid in amber tools. I could find the pdb file and when I want to add it to my system (add system dopc), I get the error which says that the argument #2 must be of type <molecule,unit,residue>.
Best, M.

    On Monday, August 24, 2015 1:36 AM, Bill Ross <> wrote:

You could look at tutorials for building new residues/molecules, and/or
look for pdb files on the net.
E.g. you could sketch one in xleap, edit the atoms and assign types from
some previous paper, loading the params in a frcmod file (read a
tutorial if this doesn't make sense). That would let you use the
molecule in Amber, but for random placement you would need other
software, and Packmol might do it, find it on the web.


On 8/23/2015 7:08 AM, mohammad roostaie wrote:
> Hi;
> I want to add DOPC lipid molecules randomly to my water-peptide system, but
> I don't know how to do it. I don't have the pdb file of lipid. What should
> I do first?
> Thanks, Mohammad.
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Received on Mon Aug 24 2015 - 10:30:06 PDT
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