VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 14:50:58 CDT

Dear All,
Just a quick followup on what I tried with "auto none" as I searched on
the web. After I included it and generated a new psf file, I got rid of
the FATAL ERROR, but the
minimization process was completely screwed up.
Is there another way to get around with it? Thank you.
Sincerely,
Margaret

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

> 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
> ------------------------------------------------------------
>

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