Re: [AMBER] ambpdb problem

From: Jio M <>
Date: Fri, 31 Jul 2009 08:11:32 +0100

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)



AMBER mailing list
Received on Wed Aug 19 2009 - 19:54:26 PDT
Custom Search