[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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