VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 13:28:47 CDT

Hi Margaret,

If you look at the topology file of CHARMM, you will
find definitions for multiple types of termini. For instance:

PRES ACE 0.00 ! acetylated N-terminus
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |

or

PRES CT1 0.00 ! methylated C-terminus from methyl acetate
GROUP ! use in generate statement
ATOM N NH1 -0.47 !
ATOM HN H 0.31 ! OT1
ATOM CA CT1 0.17 ! | //
ATOM HA HB 0.09 ! -N--CA--C HT1
ATOM C CD 0.63 ! | | \ /
ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
ATOM OT2 OS -0.34 ! \
ATOM CT CT3 -0.14 ! HT3
ATOM HT1 HA 0.09 !
ATOM HT2 HA 0.09 !
ATOM HT3 HA 0.09 !

You need to use the patch command (described in the user guide of psfgen)
in order to apply the corresponding patches (ACE, CT1, etc.) to your
protein.

Marcos

On Thu, 6 Apr 2006, Margaret Shun Cheung wrote:

> Dear John and Marcos,
>
> Thank you for the email. I looked up definitions for NTER and CTER
> and their chemical structures; this is probably not what I'd expect
> in my simulations.
> I wonder if there are options for "capped" termini, ie Acetyl and
> N-methyl options, such that charges at termini are neutral. Or is there
> another way to get around
> with charges at ends, please drop a hint.
>
> Thank you!
> Sincerely,
> Margaret
>
> On Thu, 6 Apr 2006, Marcos Sotomayor wrote:
>
>>
>> Hi Margaret,
>>
>> psfgen will build segments of your protein using a topology file which
>> defines different residues and patches. The usual CHARMM topology file
>> assumes standard protonation states for residues labeled ASP (-), GLU
>> (-), ARG (+), and LYS (+). There are three options for histidine and
>> you need to choose one of them (HSE, HSD or HSP, you may want to see
>> the first chapter of the NAMD tutorial). There are several options for
>> the termini too (charged and uncharged, etc.), which can be selected
>> through patches (which can also be used to protonate ASP and GLU, see
>> the patches PRES ACP, CTER, CT1, ASPP and GLUP in the CHARMM topology
>> file provided by VMD).
>>
>> hope that helps!
>> Marcos
>>
>> On Wed, 5 Apr 2006, John Stone wrote:
>>
>>> Hi,
>>> You'll want to read through the NAMD tutorial section
>>> about topology files, as it describes the purpose of patches
>>> for the the terminal residues:
>>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html
>>>
>>> I don't know the answer regarding charged states, you'll have to ask
>>> Jim Phillips about that, (jim_at_ks.uiuc.edu) as he wrote the psfgen.
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Tue, Apr 04, 2006 at 05:23:25PM -0400, Margaret Shun Cheung wrote:
>>>> Dear VMD wizards,
>>>>
>>>> I would like to know what kind of charged states psfgen would
>>>> generate
>>>> from a standard pdb structure.
>>>> Do I have to worry about adding charges at all?
>>>> Also, when I read the psfgen user guide, it said psfgen will
>>>> patch N-terminal and C-terminal atoms. What does "patch" means? Do
>>>> these
>>>> termini carry charges?
>>>> Thank you.
>>>> Sincerely,
>>>> Margaret S. Cheung,
>>>> Ph. D. Postdoctoral Fellow,
>>>>
>>>> ------------------------------------------------------------
>>>> Room 2117 Tel: (301) 405-4892
>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>> ------------------------------------------------------------
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>
>>
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------
>