VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Jul 31 2013 - 11:53:04 CDT

Him,

One can use any valid VMD selection text here. I assumed that the PDB file contained ONLY the ligand of interest, and hence "all" should work just fine, but there are many other selections that would yield the same result. If there were other atoms that they didn't want to modify, the selection text would need to specify the atoms of interest only.

Chris

On Jul 31, 2013, at 11:45 AM, Upadhyay, Him [him.upadhyay_at_ndsu.edu<mailto:him.upadhyay_at_ndsu.edu>] wrote:

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<mailto:him.upadhyay_at_my.ndsu.edu>
[X][X]North Dakota State University
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________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] on behalf of Mayne, Christopher G [cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>]
Sent: Wednesday, July 31, 2013 9:35 AM
To: surya narayanan chandrasekaran
Cc: <vmd-l_at_ks.uiuc.edu<mailto: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