From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Fri Jul 05 2019 - 08:23:33 CDT

Okay, I will do that.

On Fri, Jul 5, 2019 at 6:31 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> Changing the names should not change the structure... the most likely
> cause (although I cannot tell for sure unless you post the relevant files)
> is that you did not keep the columns of the pdb file properly aligned after
> changing the names. The PDB format is fixed width, so if you add a few
> characters to the name, you have to delete spaces to keep the coordinate
> columns in their proper places.
> Best,
> Peter
>
> On Fri, Jul 5, 2019 at 12:41 AM Adupa Vasista <adupavasista_at_gmail.com>
> wrote:
>
>> and also if I change the atom names as per the RTF file, then the entire
>> structure is changing.
>>
>> I am changing the Atom name in the 3rd column of the PDB.
>>
>> Thank you
>>
>>
>>
>> On Fri, Jul 5, 2019 at 3:38 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.*