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

From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Thu Jul 04 2019 - 23:54:54 CDT

The residue name of your compound is BHC in the sdf and input PDB files
while it is assigned as UNL in your output files. This is the problem in my
opinion. Change the name and make it consistent.

On Fri, 5 Jul, 2019, 9:54 AM Adupa Vasista, <adupavasista_at_gmail.com> wrote:

> 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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