[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

Fabio Affinito wrote:

This is the key part:

>> processing coordinates...
>> Warning: atom name 18113 in topol.top and out.gro does not match (MN1 
>> - CN1)
>> Warning: atom name 18114 in topol.top and out.gro does not match (MN2 
>> - CN2)
>> Warning: atom name 18115 in topol.top and out.gro does not match (N - 
>> CN3)
>> Warning: atom name 18116 in topol.top and out.gro does not match (H1 - N)
>> Warning: atom name 18117 in topol.top and out.gro does not match (H2 - 
>> CA)
>> Warning: atom name 18118 in topol.top and out.gro does not match (H3 - 
>> CB)
>> Warning: atom name 18119 in topol.top and out.gro does not match (CA - 
>> OA)
>> Warning: atom name 18120 in topol.top and out.gro does not match (HA - P)
>> Warning: atom name 18121 in topol.top and out.gro does not match (MCB1 
>> - OB)
>> Warning: atom name 18122 in topol.top and out.gro does not match (MCB2 
>> - OC)
>> Warning: atom name 18123 in topol.top and out.gro does not match (CB - 
>> OD)
>> Warning: atom name 18124 in topol.top and out.gro does not match (HB1 
>> - CC)
>> Warning: atom name 18125 in topol.top and out.gro does not match (HB2 
>> - CD)
>> Warning: atom name 18126 in topol.top and out.gro does not match (HB3 
>> - OE)
>> Warning: atom name 18127 in topol.top and out.gro does not match (C - 
>> C1A)
>> Warning: atom name 18128 in topol.top and out.gro does not match (O - 
>> O1A)
>> Warning: atom name 18129 in topol.top and out.gro does not match (N - 
>> C1B)
>> Warning: atom name 18130 in topol.top and out.gro does not match (H - 
>> C1C)
>> Warning: atom name 18131 in topol.top and out.gro does not match (CA - 
>> C1D)
>> Warning: atom name 18132 in topol.top and out.gro does not match (HA - 
>> C1E)
>> (more than 20 non-matching atom names)
>>
>> WARNING 1 [file topol.top, line 50]:
>>   219116 non-matching atom names
>>   atom names from topol.top will be used
>>   atom names from out.gro will be ignored
>>

This is the root of the problem.  Your topology does not match your coordinates 
in terms of the order of the molecules.  grompp (and, in then later, mdrun) 
thinks that protein is lipid, lipids are water, etc, so you're effectively 
telling it that things are bonded within a molecule when they're not.  Even if 
the simulation initially ran it would blow up immediately because you're mapping 
the wrong coordinates onto the wrong molecules.

The coordinate file from genconf is an exact replica of your system, but the 
molecules are not re-ordered in any convenient way.  So, for your system, 
instead of:

[ molecules ]
Protein_A	4N
Protein_B	4N
Protein_C	4N
Protein_D	4N
POPC		4N
POPG		4N
SOL		4N
K+		4N

you need this in your topology:

[ molecules ]
Protein_A	N
Protein_B	N
Protein_C	N
Protein_D	N
POPC		N
POPG		N
SOL		N
K+		N
(repeated three more times)

Otherwise, reorganize the .gro file.  Topology manipulation is probably easier, 
though.

-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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