VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 16 2018 - 15:10:45 CDT

Hi
thanks again
francesco

On Tue, Oct 16, 2018 at 5:56 PM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi,
>
> Sometimes is useful to check other patches in the CHARMM distribution. For
> instances, the DISU patch below, you need to list from which residue you
> are deleting the atoms, and from which residues belong the atoms that you
> are binding. The syntax is the residue number (1 or 2) before the atom's
> name and it matches the order of the residues that you provided in the
> command.
>
> PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and
> 2-CYS.
> ! use in a patch statement
> ! follow with AUTOgenerate ANGLes DIHEdrals command
>
> GROUP
> ATOM 1CB CT2 -0.10 !
> ATOM 1SG SM -0.08 ! 2SG--2CB--
> GROUP ! /
> ATOM 2SG SM -0.08 ! -1CB--1SG
> ATOM 2CB CT2 -0.10 !
> DELETE ATOM 1HG1
> DELETE ATOM 2HG1
> BOND 1SG 2SG
>
> I hope this helps
>
> Best
>
> João
>
>
>
> On Tue, Oct 16, 2018 at 10:47 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hi Joao
>> Thanks a lot for correcting my PRES. Now no warning in the log file about
>> either patching or improper setting, however, neither atom H91 at the
>> methylene carbon of the ligand, nor HE2 of HSP were removed, and the
>> intended bond was not formed.
>>
>> Correction to my PRES reads
>> ..........
>> DELETE ATOM H91
>> DELETE ATOM HE2
>> BOND C9 NE2
>> ! IMPR NR3 CPH1 CPH2 CG314
>> ! IMPR NR3 CPH2 CPH1 CG314
>> IMPR NE2 CD2 CE1 C9
>> IMPR NE2 CE1 CD2 C9
>>
>> Since a long time I had no need of patching. It seems that I forgot the
>> rules.
>> Thanks for advice
>>
>> francesco
>>
>> On Tue, Oct 16, 2018 at 5:21 PM João Ribeiro <jribeiro_at_ks.uiuc.edu>
>> wrote:
>>
>>> Hi Francesco,
>>>
>>> The definition of your improper angles should be done using atoms' name
>>> (e.g NE2) and not type (e.g. NE3).
>>>
>>> Best
>>>
>>> João
>>>
>>> On Tue, Oct 16, 2018 at 10:13 AM Francesco Pietra <chiendarret_at_gmail.com>
>>> wrote:
>>>
>>>> Hi
>>>> I can't understand the error message in trying to bind the sp3 carbon
>>>> C9 of a ligand to the NE2 atom of HSP residue, which implies deleting the
>>>> HE2 atom of HSP and the H91 atom at C9 of the ligand.
>>>>
>>>> PRES ZAHI 0.661 ! patch for ligand to HSP bonding
>>>>> ! use in patch statement
>>>>> ! follow with AUTOgenerate ANGles DIHEdrals
>>>>> command
>>>>> GROUP !
>>>>> ATOM C10 CG311 0.303 !
>>>>> ATOM C9 CG314 0.17 !
>>>>> ATOM H91 HGA1 0.09 !
>>>>> ATOM C8 CG2D1 0.098 ! CD2--NE2--CE1
>>>>> GROUP ! /
>>>>> ATOM CD2 CPH1 0.19 ! C10--C9--C8
>>>>> ATOM NE2 NR3 -0.51 ! |
>>>>> ATOM CE1 CPH2 0.32 ! H91
>>>>> DELETE ATOM H91
>>>>> DELETE ATOM HE2
>>>>> BOND C9 NE2
>>>>> IMPR NR3 CPH1 CPH2 CG314
>>>>> IMPR NR3 CPH2 CPH1 CG314
>>>>>
>>>>
>>>> the error message reads
>>>>
>>>> psfgen) no atom NR3 in residue HSP:227 of segment PROD
>>>>
>>>> and therefore patching failed, while the .psf file shows that NE2 of
>>>> HSP is a NR3 type atom.
>>>>
>>>> My PRES should be wrongly set. Thanks for advice.
>>>>
>>>> francesco pietra
>>>>
>>>
>>>
>>> --
>>> ……………………………………………………...
>>> João Vieira Ribeiro
>>> Theoretical and Computational Biophysics Group
>>> Beckman Institute, University of Illinois
>>> http://www.ks.uiuc.edu/~jribeiro/
>>> jribeiro_at_ks.uiuc.edu
>>> +1 (217) 3005851
>>>
>>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>