[gmx-users] Zwitterionic amino acid topology parameters in CHARMM
Justin Lemkul
jalemkul at vt.edu
Wed Oct 31 21:52:55 CET 2018
On 10/31/18 4:23 PM, rose rahmani wrote:
> i've tried it.But the results are exactly the same as i didn't apply
> patches. it doesn't make any difference. So what is the purpose of using
> -ter (COO- & NH3) when results are same in my case?
I don't follow. Topology generation requires the selection of terminal
patching of some sort, either if pdb2gmx does it for you (choosing
defaults) or if you do it.
-Justin
> On Wed, 31 Oct 2018, 22:49 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 10/31/18 2:56 PM, rose rahmani wrote:
>>> Thank you, but I couldn't understand you exactly. My structures already
>>> have NH3+ and COO- . You mean everything is right? That's normal, yes?
>> I was stating which terminal patches you should choose with pdb2gmx to
>> transform the Phe .rtp topology into that of a zwitterion.
>>
>> -Justin
>>
>>> On Wed, 31 Oct 2018, 21:43 Justin Lemkul, <jalemkul at vt.edu> wrote:
>>>
>>>> On 10/31/18 2:01 PM, rose rahmani wrote:
>>>>> Hi,
>>>>>
>>>>> I want to use zwitterionic form of AAs in CHARMM ff. I gave structure
>> in
>>>>> Discovery studio and then use pdb2gmx to get its topology and ...
>> files.
>>>>> But the number of atoms in topol.top and also some atom's partial
>> charges
>>>>> are different from atoms and charges in aminoacids.rtp
>>>>> For example, in the case of phenylalanine,
>>>>> this is topology file after pdb2gmx:
>>>>>
>>>>> [ atoms ]
>>>>> ; nr type resnr residue atom cgnr charge mass
>>>> typeB
>>>>> chargeB massB
>>>>> ; residue 1 PHE rtp PHE q 0.0
>>>>> 1 NH3 1 PHE N 1 -0.3 14.007
>> ;
>>>>> qtot -0.3
>>>>> 2 HC 1 PHE H1 2 0.33 1.008
>> ;
>>>>> qtot 0.03
>>>>> 3 HC 1 PHE H2 3 0.33 1.008
>> ;
>>>>> qtot 0.36
>>>>> 4 HC 1 PHE H3 4 0.33 1.008
>> ;
>>>>> qtot 0.69
>>>>> 5 CT1 1 PHE CA 5 0.21 12.011
>> ;
>>>>> qtot 0.9
>>>>> 6 HB 1 PHE HA 6 0.1 1.008
>> ;
>>>>> qtot 1
>>>>> 7 CT2 1 PHE CB 7 -0.18 12.011
>> ;
>>>>> qtot 0.82
>>>>> 8 HA 1 PHE HB1 8 0.09 1.008
>> ;
>>>>> qtot 0.91
>>>>> 9 HA 1 PHE HB2 9 0.09 1.008
>> ;
>>>>> qtot 1
>>>>> 10 CA 1 PHE CG 10 0 12.011
>> ;
>>>>> qtot 1
>>>>> 11 CA 1 PHE CD1 11 -0.115 12.011
>> ;
>>>>> qtot 0.885
>>>>> 12 HP 1 PHE HD1 12 0.115 1.008
>> ;
>>>>> qtot 1
>>>>> 13 CA 1 PHE CE1 13 -0.115 12.011
>> ;
>>>>> qtot 0.885
>>>>> 14 HP 1 PHE HE1 14 0.115 1.008
>> ;
>>>>> qtot 1
>>>>> 15 CA 1 PHE CZ 15 -0.115 12.011
>> ;
>>>>> qtot 0.885
>>>>> 16 HP 1 PHE HZ 16 0.115 1.008
>> ;
>>>>> qtot 1
>>>>> 17 CA 1 PHE CD2 17 -0.115 12.011
>> ;
>>>>> qtot 0.885
>>>>> 18 HP 1 PHE HD2 18 0.115 1.008
>> ;
>>>>> qtot 1
>>>>> 19 CA 1 PHE CE2 19 -0.115 12.011
>> ;
>>>>> qtot 0.885
>>>>> 20 HP 1 PHE HE2 20 0.115 1.008
>> ;
>>>>> qtot 1
>>>>> 21 CC 1 PHE C 21 0.34 12.011
>> ;
>>>>> qtot 1.34
>>>>> 22 OC 1 PHE OT1 22 -0.67 15.999
>> ;
>>>>> qtot 0.67
>>>>> 23 OC 1 PHE OT2 23 -0.67 15.999
>> ;
>>>>> qtot 0
>>>>>
>>>>> and this is .rtp file for PHE:
>>>>>
>>>>> [ PHE ]
>>>>> [ atoms ]
>>>>> N NH1 -0.47 0
>>>>> HN H 0.31 1
>>>>> CA CT1 0.07 2
>>>>> HA HB 0.09 3
>>>>> CB CT2 -0.18 4
>>>>> HB1 HA 0.09 5
>>>>> HB2 HA 0.09 6
>>>>> CG CA 0.00 7
>>>>> CD1 CA -0.115 8
>>>>> HD1 HP 0.115 9
>>>>> CE1 CA -0.115 10
>>>>> HE1 HP 0.115 11
>>>>> CZ CA -0.115 12
>>>>> HZ HP 0.115 13
>>>>> CD2 CA -0.115 14
>>>>> HD2 HP 0.115 15
>>>>> CE2 CA -0.115 16
>>>>> HE2 HP 0.115 17
>>>>> C C 0.51 18
>>>>> O O -0.51 19
>>>>> so as you see there O and 2 H more... . I know that's because of COO
>>>> group
>>>>> and HH.. but which of them are the real structure of zwitterionic form
>> of
>>>>> amino acid in force field? are both true? I would be appreciated if
>> you
>>>>> can help me.
>>>> Just apply the normal NH3+ and COO- terminal patches. There are no
>>>> special zwitterion patches like in some force fields (OPLS, etc.)
>>>> Naturally, the .rtp will change - that is the function of the .tdb
>> entries.
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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