[gmx-users] Simulating Multiple Solute Particles

[Justin Lemkul]

On 11/3/14 12:50 AM, Nathan K Houtz wrote:
> Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said:
>
>> Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem... at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>
> Thank you Justin! I think it's easier to just paste it here. This is my topol.top file:
>
>> [ defaults ]
>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>   1             2               yes              0.5     0.5
>>
>> [ atomtypes ]
>> ;name	at.num      mass     charge  ptype       sigma           epsilon
>>   CH3       15   15.03500    0.000      A       0.39100         0.66944 ;united atom Methyl [C-CH3]
>>     C       12   12.01100    0.000      A       0.35000         0.27614 ;C [R3CCOO-] (first carbon)
>>    CM       12   12.01100    0.000      A       0.37500         0.43932 ;carboxyl C [R-(C=O)-OH]
>>     O        8   15.99940    0.000      A       0.30800         0.71128 ;carboxyl O [C-O-H]
>>    OM        8   15.99940    0.000      A       0.29600         0.87864 ;carbonyl O [C=O]
>>     H        1    1.00794    0.000      A       0.00000         0.00000 ;carboxyl H [C-O-H]
>>    OW        8   15.99940    0.000      A       0.31660         0.65000
>>    HW        1    1.00794    0.000      A       0.00000         0.00000
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>>   TETR            3
>>
>> [ atoms ]
>> ;   nr    type   resnr  residu    atom    cgnr  charge     mass
>>      1     CH3       1    TETR      C1       1   0          15.03500
>>      2       C       1    TETR      C2       1   0          12.01100
>>      3       C       1    TETR      C3       1   0          12.01100
>>      4      CM       1    TETR      C4       1   0.38       12.01100
>>      5      OM       1    TETR      O1       1  -0.38       15.99940
>>      6       O       1    TETR      O2       1  -0.40       15.99940
>>      7       H       1    TETR      H4       1   0.40        1.00794
>>
>> [constraints]
>> ;   i       j       funct       distance
>>     1       2           1        0.14550
>>     2       3           1        0.11780
>>     3       4           1        0.14420
>>     4       5           1        0.12040
>>     4       6           1        0.13100
>>     6       7           1        0.89000
>>
>> ; Include SPC water topology
>> #include "oplsaa.ff/tip3p.itp"
>>

Here's your problem.  Look at the contents of tip3p.itp:

[ atoms ]
; id    at type res nr  residu name at name     cg nr   charge
1     opls_111  1       SOL              OW             1       -0.834
2     opls_112  1       SOL             HW1             1        0.417
3     opls_112  1       SOL             HW2             1        0.417

It uses OPLS-AA atom types, but you haven't defined what those are because 
nothing above calls the OPLS-AA force field.  Hence, grompp dies because it does 
not know how to assign nonbonded parameters to opls_111 or opls_112.

>> [ system ]
>> Tetrolic Acid in water
>>
>> [ molecules ]
>> Tetrolic Acid	  500
>> SOL              5481
>
> I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well?
>

Topologies do not have the same formatting requirements.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================