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

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Fri Jul 05 2019 - 00:04:32 CDT

*BHC *is the compound name BENZENE HEXACARBOXYLIC ACID
you can see that the residue name in RTF is assigned as UNL. so I think the
problem is not with resname.

On Fri, Jul 5, 2019 at 10:25 AM Pratik Narain Srivastava <
pratik.narain_at_gmail.com> wrote:

> 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.*
>>
>

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

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