[gmx-users] (no subject)
Justin Lemkul
jalemkul at vt.edu
Tue Nov 19 17:39:39 CET 2013
On 11/19/13 11:31 AM, Mohsen Ramezanpour wrote:
> Hi
> I think you should use the correct atomtype, accoding to this FF
> atomtypes, for your atom which you have introduced as HH.
>
Correct. More explicitly, the trick to dealing with OPLS-AA is that its
nonbonded types (opls_*) have bonded equivalents that are defined in
ffnonbonded.itp. The problem with the [ *types ] directives shown below is
(first) that they use atom names instead of types and (second) that the strings
are interpreted as types and do not correspond to the desired parameters.
The atom named "HH" has a nonbonded type opls_168, so its bonded type (thus what
must be used in ffbonded.itp when defining interactions is "HO," not "HH."
-Justin
> On Tue, Nov 19, 2013 at 7:48 PM, fatemeh ramezani <fr_750 at yahoo.com> wrote:
>
>> HI DEAR USERS
>> I want to simulate collagen by OPLSAA. I added hydroxyprolin parameters as
>> follow:
>>
>> in .hdb file :
>>
>> HYP 5
>> 1 5 HA CA N C CB
>> 2 6 HB CB CG CA
>> 1 6 HG CG CD CB
>> 1 6 HD CD N CG
>> 1 4 HH OH CG CD
>>
>>
>> in aminoacids.c.tdb file:
>> [ HYP-COO- ]
>> [ replace ]
>> CA CA opls_285 12.011 -0.09
>> C C opls_271 12.011 0.7
>> O O1 opls_272 15.9994 -0.8
>> OXT O2 opls_272 15.9994 -0.8
>> [ add ]
>> 2 8 O C CA N
>> opls_272 15.9994 -0.8
>> [ impropers ]
>> CA O1 C O2 improper_O_C_X_Y
>>
>> [ HYP-ZWITTERION_COO- ]
>> [ replace ]
>> CA CA opls_246 12.011 0.13
>> C C opls_271 12.011 0.7
>> O O1 opls_272 15.9994 -0.8
>> OXT O2 opls_272 15.9994 -0.8
>> [ add ]
>> 2 8 O C CA N
>> opls_272 15.9994 -0.8
>> [ impropers ]
>> CA O1 C O2 improper_O_C_X_Y
>>
>>
>>
>> in aminoacids.n.tdb file:
>>
>> [ HYP-COO- ]
>> [ replace ]
>> CA CA opls_285 12.011 -0.09
>> C C opls_271 12.011 0.7
>> O O1 opls_272 15.9994 -0.8
>> OXT O2 opls_272 15.9994 -0.8
>> [ add ]
>> 2 8 O C CA N
>> opls_272 15.9994 -0.8
>> [ impropers ]
>> CA O1 C O2 improper_O_C_X_Y
>>
>> [ HYP-ZWITTERION_COO- ]
>> [ replace ]
>> CA CA opls_246 12.011 0.13
>> C C opls_271 12.011 0.7
>> O O1 opls_272 15.9994 -0.8
>> OXT O2 opls_272 15.9994 -0.8
>> [ add ]
>> 2 8 O C CA N
>> opls_272 15.9994 -0.8
>> [ impropers ]
>> CA O1 C O2 improper_O_C_X_Y
>>
>>
>> in aminoacids.rtp file:
>> [HYP]
>> [ atoms ]
>> N opls_239 -0.140 1
>> CA opls_246 0.010 1
>> HA opls_140 0.060 1
>> CB opls_136 -0.120 2
>> HB1 opls_140 0.060 2
>> HB2 opls_140 0.060 2
>> CG opls_136 -0.120 3
>> HG1 opls_140 0.060 3
>> OH opls_167 -0.683 3
>> HH opls_168 0.435 3
>> CD opls_245 -0.050 4
>> HD1 opls_140 0.060 4
>> HD2 opls_140 0.060 4
>> C opls_235 0.500 5
>> O opls_236 -0.500 5
>> [ bonds ]
>> N CA
>> CA HA
>> CA CB
>> CA C
>> CB HB1
>> CB HB2
>> CB CG
>> CG HG1
>> CG OH
>> OH HH
>> CG CD
>> CD HD1
>> CD HD2
>> CD N
>> C O
>> -C N
>> [ impropers ]
>> -C CA N CD improper_Z_N_X_Y
>> CA +N C O improper_O_C_X_Y
>>
>> in ffbonded.itp file:
>> [ angletypes ]
>> ; i j k func th0 cth
>> CG CB OH 2 109.5 520.0
>> OH CG CD 2 109.5 520.0
>> CG OH HH 2 109.5 450.0
>>
>> [ dihedraltype ]
>> CG CB CD OH 1 35.3 334.8
>>
>> CB CG OH HH 1 0.0 1.3 3
>>
>>
>> [ bondtype ]
>> CG OH 2 0.144 6100000.0 ;
>>
>> OH HH 2 0.100 15700000.0 ;
>>
>>
>> When I grompp, I get this error:
>> Unknown bond_atomtype HH
>> What does this error mean ?
>>
>>
>> Fatemeh Ramezani
>> --
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--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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