VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 14:11:54 CDT

Dear All,

I tried it with psfgen using the syntax in (1). But when
I tried to minimize the structure, namd gave me another error in (2).
Do I miss something in the psfgen input file? Thank you!
Sincerely,
Margaret

(1)
segment A {
pdb my.pdb
         first ACE
         last CT1
}

(2)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB

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

>
> Dear All,
> Thank you very much for the tips!
> Sincerely,
> Margaret
>
> On Thu, 6 Apr 2006, Peter Freddolino wrote:
>
>> Dear Margaret,
>> you may want to look at some of the other patches that Marcos
>> mentioned in his email, such as ACE (acetylated N terminus) or CT1
>> (methylated C terminus). They are all present in the topology file.
>> Best,
>> Peter
>>
>> 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
>>> ------------------------------------------------------------
>>
>
> 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
> ------------------------------------------------------------
>

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
------------------------------------------------------------