VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Oct 16 2018 - 10:56:05 CDT

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