From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Mar 29 2016 - 08:11:27 CDT

Hi Abhishek,

I am not entirely familiar with MC simulation, but I do know for a fact
that you need topology files for run MD simulations. If it is polyethelene,
I am guessing you would only need ethylene parameters, which is available
in the top_all36_cgenff.rtf file of the CHARMM 36 force field package. You
can download them from here

http://mackerell.umaryland.edu/charmm_ff.shtml

Once you have that, simply follow the procedure of generating a PSF file
described in the namd manual. You basically need to use the psfgen command.

Hope this helps,
Chitrak.

On Mon, Mar 28, 2016 at 1:41 AM, ABHISHEK GUPTA <akgiitm_at_gmail.com> wrote:

> Dear Chitrak
> I don't have the topology file for my system. I have generated the
> coordinates of the polymer chains using an algorithm and tried to visulaize
> in VMD. I'm trying to do the MC simulation of my configuration. If I'm not
> having the topology file and only the PDB, then how to generate the PSF for
> the PDB. Can you please share the script you are using to generate PSF
> file for the PDB ?
> Please reply.
>
> Best regards
> Abhishek
>
> On Mon, Mar 21, 2016 at 3:57 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Hi Abhishek,
>>
>> Look through the "Generating a Protein Structure File (PSF)" section of
>> the NAMD tutorial (VMD also has a automatic PSF generator, but I am
>> slightly old-fashioned in this, I still use the script). I am assuming you
>> already have topology files for your system. With that and the PDB file,
>> you should be able to generate a PSF file and view the molecule in VMD.
>>
>>
>> Hope this helps,
>> Chitrak.
>>
>> On Sat, Mar 19, 2016 at 1:06 AM, ABHISHEK GUPTA <akgiitm_at_gmail.com>
>> wrote:
>>
>>> Thankyou Norman & John,
>>>
>>> As you told me to build a psf file in VMD for clearly seeing only the
>>> bonded atoms without showing bonds between unbonded atoms,
>>> I have tried to build a psf file for my PDB from a code in VMD site but
>>> the code that converts the CONECT info in VMD to PSF file is given in binary
>>> and i couldn't understand how to use it.
>>> Can you please answer how to create a psf file for my PDB coordinate
>>> file for polyetylene chains so that i will be able to visualize my
>>> structure properly
>>> without bonding between the unbonded atoms ?
>>>
>>> Thanks and Regards
>>>
>>> On Wed, Mar 16, 2016 at 9:55 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>
>>>> Hi,
>>>> Perhaps I'm missing something, but VMD does read and process the
>>>> PDB "CONECT" records when they are present, but this only works when
>>>> the atom count is less than 99,999, as per the spec:
>>>> http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_69.html
>>>>
>>>> I should also note that the PDB CONECT records are intended only for
>>>> "special" bonds, e.g. disulfide, that would not normally be guessed
>>>> by simple distance-based heuristics.
>>>>
>>>> If your structure comes from the PDB, you could try using the "autopsf"
>>>> plugin in VMD to have it try and complete the structure (and bonds) for
>>>> you.
>>>>
>>>> Cheers,
>>>> John
>>>>
>>>> On Wed, Mar 16, 2016 at 10:56:34AM +0100, Norman Geist wrote:
>>>> > If VMD doesn't get any bond information from any input file, it
>>>> will guess
>>>> > bonds for visualization purpose. This guessing is done based on
>>>> elements
>>>> > vdw radii but before the elements are guessed from atom names, if
>>>> also
>>>> > this information is not available. If you have overlapping
>>>> polymers which
>>>> > VMD should not show to be bonded, you need to tell VMD where to
>>>> draw the
>>>> > bonds. This can be done from the TCL interface or by passing a
>>>> suitable
>>>> > parameter file, which describes your system e.g. prmtop or psf.
>>>> > Unfortunately VMD doesn't care about either the connectivity table
>>>> in PDB
>>>> > files nor the TER lines.
>>>> >
>>>> >
>>>> >
>>>> > Norman Geist
>>>> >
>>>> >
>>>> >
>>>> > Von: ABHISHEK GUPTA [mailto:akgiitm_at_gmail.com]
>>>> > Gesendet: Mittwoch, 16. Maerz 2016 08:35
>>>> > An: Norman Geist <norman.geist_at_uni-greifswald.de>
>>>> > Betreff: Re: vmd-l: Unable to visualize my polymer chains
>>>> generated using
>>>> > RIS theory using VMD properly
>>>> >
>>>> >
>>>> >
>>>> > What do you mean by saying "Proper bond information" ?
>>>> >
>>>> > KIndly clarify
>>>> >
>>>> > I was giving the bond connectivity information at the lower of the
>>>> PDB
>>>> > file to show the connectivity.
>>>> >
>>>> > Is this problem due to steric hindrance of the non-bonded atoms in
>>>> > polyethylene chain ? Does VMD chose some distance criterion to
>>>> connect
>>>> > atoms ?
>>>> >
>>>> > Regards
>>>> >
>>>> > Abhishek
>>>> >
>>>> >
>>>> >
>>>> > On Tue, Mar 15, 2016 at 1:23 PM, Norman Geist
>>>> > <[1]norman.geist_at_uni-greifswald.de> wrote:
>>>> >
>>>> > If the atoms are that close, you won't get any reasonable bond
>>>> guessing
>>>> > at all. You may want to supply a parameter file to VMD which
>>>> contains
>>>> > the proper bond information.
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > Norman Geist
>>>> >
>>>> >
>>>> >
>>>> > Von: [2]owner-vmd-l_at_ks.uiuc.edu [mailto:[3]
>>>> owner-vmd-l_at_ks.uiuc.edu] Im
>>>> > Auftrag von ABHISHEK GUPTA
>>>> > Gesendet: Samstag, 12. Maerz 2016 04:10
>>>> > An: [4]vmd-l_at_ks.uiuc.edu
>>>> > Betreff: vmd-l: Unable to visualize my polymer chains generated
>>>> using
>>>> > RIS theory using VMD properly
>>>> >
>>>> >
>>>> >
>>>> > Hello,
>>>> >
>>>> > I am trying to visualize the simple polyethylene chains (multiple
>>>> > chains) consisting of certain number of atoms generated using
>>>> RIS theory
>>>> > using VMD. I'm using the PDB format to express coordinates to
>>>> visualize
>>>> > my chains. The chains are very random and at some points
>>>> multiple atoms
>>>> > of a chain comes very near to each other. Sometimes, even there
>>>> is inter
>>>> > chain overlapping and multiple atoms of different chains comes
>>>> in close
>>>> > vicinity of each other. In such a situation, while visualizing
>>>> via. VMD,
>>>> > there appears a bond between those close or very close atoms
>>>> within a
>>>> > chain or between two chains. Therefore, the visulaization by VMD
>>>> shows
>>>> > that number of bonds is much greater than the number of atoms
>>>> and forms
>>>> > a cage like structure (in some cases) between the closely spaced
>>>> or
>>>> > overlapping atoms. What might be the possible cause of this ?
>>>> Does VMD
>>>> > connects Atoms taking in some distance criterion ? Can we change
>>>> that
>>>> > distance criteria that VMD utilize to connect the atoms of a
>>>> polymer
>>>> > chain in succession ?
>>>> >
>>>> > Thanks and Regards
>>>> >
>>>> > Abhishek Kumar Gupta
>>>> >
>>>> >
>>>> >
>>>> > References
>>>> >
>>>> > Visible links
>>>> > 1. mailto:norman.geist_at_uni-greifswald.de
>>>> > 2. mailto:owner-vmd-l_at_ks.uiuc.edu
>>>> > 3. mailto:owner-vmd-l_at_ks.uiuc.edu
>>>> > 4. mailto:vmd-l_at_ks.uiuc.edu
>>>>
>>>> --
>>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>>> http://www.ks.uiuc.edu/Research/vmd/
>>>>
>>>
>>>
>>
>