AMBER Archive (2009)

Subject: Re: [AMBER] ambpdb problem

From: Jordan Monnet (monnet.jordan_at_free.fr)
Date: Fri Jul 31 2009 - 09:30:54 CDT

Hello!

I do not know anything about MOE or SYBYL but since the charges are in
the pqr file, they are here.

I think you have made a prep file (or a mol2) for leap to build your
topo/coords to run you simulation? Charges must be here (in prep or
mol2) whether they are, you no not have to worry.

You can do your docking with any visulisation program you want then, save
a pdb (or mol2), load it into leap build your topo/coords and it should be fine.
If you want to check, you can make a pqr file from you topo/coords and
see whether the charges are correct. You can also check your topo file
with rdparm (see http://www.chpc.utah.edu/~cheatham.rdparm.html)

--jordan
 
* Jio M (jiomm_at_yahoo.com) wrote:
> Thanks Ashish and Jordan for the reply,
>
>
>
> I used the same command with additional -pqr. I got the pqr file with
> charges :-). these are the same charges that I derived as RESP charges thats what I needed
>
>
>
> 1) I saved .pqr file as .pdb file by gedit, that is the text file. When
> I visualised the pdb file in MOE,SYBYL to look for the charges I didnt
> see charges on atoms (all shown as 0.0000) :-(
>
> but the charges are there if I see the pdb file as a text file
>
>
>
> 2) secondly I dont know how it worked with loadpdb
>
> p = loadpdb myfile.pqr
>
> edit p
>
> again if I see in xleap no charge is displayed.
>
> 3) reason for need of charges is that I want to dock this structure with some else different molecule. this require charges.
>
> what can be the reason that in text file of .pqr (hence .pdb file)
> charges are there but not displayed in any (MOE,SYBYL) visualiser. can
> I use the pdb file for docking procedures even though I cannot see
> charges in visualiser because the calculations are performed by using
> the text in file (pls correct me if am wrong)
>
>
>
> thanks
>
>
>
> Jio
>
>
>
>
>
>
>
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    }><(({*>
__/

Jordan MONNET
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
Phone: +336 20 70 24 93

http://monnet.jordan.free.fr/

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