[gmx-users] position restrain

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> parto haghighi wrote:
>> Dear GMX users,
>> I am working on lipid_drg system
>> my drug molecule has 23 atoms.
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> DRG      3
>>
>> [ atoms ]
>> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>>      1       CH3     1  DRG     CAA     1   -0.073  15.0350
>>      2       CH2     1  DRG     CAH     2    0.115  14.0270
>>      3       CH2     1  DRG     CAI     3    0.367  14.0270
>>      4        NL     1  DRG       N     4   -0.448  14.0067
>>      5         H     1  DRG      H1     5    0.346   1.0080
>>      6         H     1  DRG      H2     6    0.367   1.0080
>>      7       CH1     1  DRG      CA     7    0.297  13.0190
>>      8       CH3     1  DRG      CB     8    0.000  15.0350
>>      9         C     1  DRG       C     9    0.743  12.0110
>>     10         O     1  DRG       O    10   -0.598  15.9994
>>     11         N     1  DRG     NAK    11   -0.776  14.0067
>>     12         H     1  DRG     HAK    12    0.400  1.0080
>>     13         C     1  DRG     CAP    13    0.470  12.0110
>>     14       CR1     1  DRG     CAG    14    0.157  12.0110
>>     15       CH3     1  DRG     CAL    15   -0.072   1.0080
>>     16       CR1     1  DRG     CAF    16   -0.309  12.0110
>>     17        HC     1  DRG     HB4    17    0.253  1.0080
>>     18         S     1  DRG     SAM    18    0.089  32.0600
>>     19         C     1  DRG     CAQ    19   -0.508  12.0110
>>     20         C     1  DRG     CAN    20    0.968  12.0110
>>     21         O     1  DRG     OAD    21   -0.619  15.9994
>>     22        OA     1  DRG     OAL    22   -0.347  15.9994
>>     23       CH3     1  DRG     CAB    23    0.178  15.0350
>>

Side note - this topology does not appear to be sufficiently correct for use 
with 43A1.  The charges are all odd values and the charge groups are not set 
correctly.  I suspect you should spend some time doing significant 
reparameterization before doing any real simulations, otherwise you may spend a 
large amount of time to end up with junk.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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