Message: 2
Date: Mon, 30 Jan 2012 07:26:59 +0100
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] loading of fullerene2160
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20120130072659.4rn75t40g8swo804.webmail.u-picardie.fr>
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Dear Gargi Borgohai,
> Thank you for your reply. I am using AMBER10. The
> problem is that I am not even able to load the molecule in xLeap. The pdb
> file of fullerene C60 can be loaded, but without
> bond connectivity . Loading of frcmod and prepin files solve this problem.
the "bondbydistance" command should add the bonds to a molecule loaded
in the PDB file format...
x = loadpdb fullereneXXX.pdb
bondbydistance x
> But the problem arises with giant fullerenes like C720 and C2160. I think
> the problem is related to frcmod and prepin files which I am not able to
> generate for these molecules.
for each new molecule/molecular fragment you need to create a force
field library in a file format (off, prep, mol2 or mol3; see
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php)
> To the best of my knowledge, antechamber can
> not be used for molecules with large number of atoms.
I think antechamber deals with large molecules; the key here is not
the size of the molecule but chemical equivalencing... I am not sure
Ante_R.E.D. 2.0 can handle this type of molecule...
> So please let me
> know how to load the pdb files of these molecules and save the prmtop
files.
You first need to create a force field library with atom
connectivities, charge value(s), atom type(s) and atom names.
if you decide to use R.E.D., I would create a P2N file with identical
atom names in the 1st column of atom names.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
Finally, I would first check in literature...
regards, Francois
> Dear Gargi Borgohai,
>
>> I have the pdb file of fullerene2160. I am trying to
>> load the molecule, save the parameters and to give a homogenous charge
>> distrbution on all the carbon atoms. Will you please let me know how can
i
>> do it successfully.
>
> If you consider all the carbon atoms of your fullerene chemically
> equivalent (as they should be - to be checked) and if the total charge
> of your molecule is zero, this likely means the charge value of each
> carbon equals zero.
>
> I would check what charge values are used in the literature for your
> molecule or similar ones...
>
> regards, Francois
Respected Sir,
I followed the tutorial for R.E.D. At first
Ante_R.E.D. program was executed to convert pdb file to p2n file. Using
.p2n and .log input files when I run R.E.D. the following comments appear:
WARNING:
A unique atom name column is detected
The atom names in the PDB (& Tripos) file(s) will be incremented
WARNING:
No three atom based re-orientation found in the P2N file
Re-orientation will be done according to the GAUSSIAN Algorithm!
* Selected QM Software *
GAUSSIAN
* Software checking *
Gaussian [ NOT FOUND ]
resp [ NOT FOUND ]
ERROR: Some program(s) cannot be executed
Sir how should I proceed to get the mol2 file successfully.
Thanking you,
Sincerely
Gargi Borgohain
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Received on Mon Feb 06 2012 - 05:30:04 PST
