Re: vmd-l:namd-l; question about psfgen (param for CT1?)

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 15:53:20 CDT

Dear VMD and NAMD users,
Sorry for this lengthy email. I was advised to spread this email list
to NAMD-L about parameter for CT1, a methylated C-term).
I followed procedures to include a methylated C-term using psfgen ({auto
angles dihedrals}).
But when I minimize it using "par_all27_prot_lipid.inp", then
NAMD generates a FATAL error in (2).

Did I miss something in my psfgen or namd parameters?
Thank you.
Sincerely,
Margaret

On Thu, 6 Apr 2006, Peter Freddolino wrote:

> Hi Margaret,
> what parameter file are you using? The error you get (2) indicates
> that you don't have parameters for some piece of what you're
> simulating (likely one of the nonstandard terminii). Please let us
> know. You may also want to move the discussion to NAMDL if you have
> further questions about this.
> Best,
> Peter
>
> Margaret Shun Cheung wrote:
>
>>
>> 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
>> ------------------------------------------------------------
>

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:29 CST