[gmx-users] Zwitterionic amino acid topology parameters in CHARMM
Justin Lemkul
jalemkul at vt.edu
Wed Oct 31 20:19:12 CET 2018
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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--
==================================================
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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