Hello,

On Mon, Jan 18, 2010 at 5:06 AM, matteo.rotter <matteo.rotter@uniud.it> wrote:
Thanks a lot for your help!
now works.
So i have some more questions:

The charge value in the param file come from the psf, so same atoms of same residues, but in  different position of the structure could have different  charge.  Using a single value for that atom is not a problem because apolar calc need only radius and well-depth value?

Could you be more specific please? What do you mean by "in  different position of the structure could have different  charge"?
 
and also, you say that there is no need to have duplicate atom entries, but there are a lot of repetitions in the file that you sent me. For example the PRO residue  is repeated some times. So i've tried to erase the duplicated lines ( sort -k  2  | uniq)  and  the calculation didn't work. So i tried to resort this param file without repetitions according to the first column
and now it works.

I cleaned redundant ILE residues in your param.prm file, but didn't do it for the other residues in the file, because such a manual cleaning took too much time, and apparently only the redundant ILE residues in the param.prm file caused your original problem. However, it is recommended to do the cleaning for all other residues.

Thanks,

Yong
 
 
Still remains the doubt for the charge value.


Thanks in advance,
Regards,
Matteo.

Yong Huang ha scritto:
Hello,

Parm file is like a look-up table, telling the program to look up atom parameters from this table when needed. Therefore in this look-up table, there is no need to have duplicate atom entries. For instance, only one ILE residue is needed in the parm file with complete list of ILE atoms and parameters. 

I've modified your param.prm and apbs.in files acoordingly (please see the attachments), which should get things going now.

Thanks,

Yong


On Sat, Jan 16, 2010 at 2:06 AM, matteo.rotter <matteo.rotter@uniud.it> wrote:
Hi
following: the apbs .in file


read
    mol pqr ppp.pqr
    parm flat param.prm2
end

APOLAR  name solvated
        grid 0.3 0.3 0.3
        mol 1
        srfm sacc
        swin 0.3
        srad 0.65
        press 0.2394
        gamma 0.0085
        bconc 0.033428
        sdens 100.0
        dpos 0.2
        temp 298.15
        calcenergy total
        calcforce comps
END

print apolEnergy solvated end
print apolForce solvated end
quit

Thanks a lot!
Regards, Matteo.





Yong Huang ha scritto:
Hello,

Could you please send us the APBS input file that you had problem with, so that we can locate such a problem?

Thanks,

Yong



-------- Original Message --------
Subject: Apolar parameter.
Date: Fri, 15 Jan 2010 18:00:57 +0100
From: matteo.rotter <matteo.rotter@uniud.it>
To: Nathan Baker <baker@biochem.wustl.edu>
CC: apbs-users <apbs-users@lists.sourceforge.net>

Dear all,
I have a problem to use the apolar calculation of APBS.
The matter is the param file. I have created the pqr and the parameter
file from pdb following the direction of the documentation. The pqr
works fine for the elec calculation, but the apolar does not work due to
the error 'unable to find atom ..'
So I need some informations: the order of the atom in param file must be
the same that the one in pqr file? Or there are some more information
that i miss? Other apolar calculations with other structures and param
file created in the same way work, so i am a bit confused. In attachment
pdb, pqr, param(with same atom sorting of pqr), param2(more param | sort
-k 2 | uniq)

Thanks in advance,
Regards,
Matteo


--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine




--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine




--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine