Re: Re: vmd-l: Getting the topology,PSF files

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Thu Jul 04 2019 - 23:22:37 CDT

yeah, i have changed those but still the problem exists.

On Fri, Jul 5, 2019 at 3:40 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> Dear Adupa,
> Did you try following the advice that was given in response to your prior
> emails, of ensuring that the atom names in your .pdb file match those from
> the ATOM entries in your .rtf file? If so, that is certainly not reflected
> in the input pdb that you have posted...
> Best,
> Peter
>
> On Thu, Jul 4, 2019 at 5:16 PM Adupa Vasista <adupavasista_at_gmail.com>
> wrote:
>
>> I have been facing this problem since last week,
>> 1) I have taken a Ligand which is SDF format and converted in PDB using
>> openbabel.
>> 2) uploaded to LigParGen/CGenFF to get the topology files. I got the
>> topology files.
>>
>> 3) I opened the PDB in VMD and Using the RTF file generated by
>> LigParGen/CGenFF in AutoPSF; I got psf and PDB.
>>
>> 4) when I look at the PDB generated by Autopsf all the coordinates are
>> alike, and I am getting a single atom when I load it in VMD.
>>
>>
>> Here I attach all the related files; please look into it.
>>
>> Attached files 1) 1.sdf from the internet
>> 2) 1.pdb using OpenBabel
>> 3)1_autopsf.pdb and psf which are generated
>> by AutoPSF
>> 4) RTF file generated by LigParGen (CHARMM
>> force field)
>>
>>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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