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From: Upadhyay, Him [him.upadhyay_at_ndsu.edu] ([him.upadhyay_at_ndsu.edu)
Date: Wed Jul 31 2013 - 11:45:23 CDT
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Hi Chris,
we can also edit using molefacture by loading pdb file by typing "not water" instead "all" in the same popup window. Is there any difference by typing "all" instead "not water" ?
Him
________________________________
Him Upadhyay
Ehly 120
Phone: 701-231-6275
him.upadhyay_at_my.ndsu.edu
[X][X]North Dakota State University
[X][X]
________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Mayne, Christopher G [cmayne2_at_illinois.edu]
Sent: Wednesday, July 31, 2013 9:35 AM
To: surya narayanan chandrasekaran
Cc: <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: bypassing MolFrac step
Surya,
When starting up Molefacture there is a popup window in which you can specify a selection of the structure to load, e.g., type "all" in this box followed by clicking on the "Start Molefacture" button.
Regards,
Christopher Mayne
Upon starting
On Jul 31, 2013, at 5:50 AM, surya narayanan chandrasekaran wrote:
hi,
this regarding first step in FFTK If i have already a PDB file, if i load in VMD then go for Molfrac step the first step used to give atom types and psf file generation. the molecule disappears. I don't want to make a new structural generation because the alignment of molecule is so important to me. so kindly help me in this regard how can i give the PDB file as input to generate PSF file.
Thank you
-- Suryanarayanan C M.S Chemist 01742857830
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