[gmx-users] Gro file does not match topology file... continue

[Justin Lemkul]

On 1/27/17 11:45 AM, Poncho Arvayo Zatarain wrote:
>
>
> Hello: according to the queshere abouttion and the answer send me here about gro (58674) file does not mtch with the topology (58666), i checked my gro file at the top corner on the left and said 58674, and at the end of the file the number of molecules is the same, 58674. i used TIP3 model and 2 phospholipids: 26 dppe and 230 dppe also 8960 of TIP3.
> My top file is
> : Include forcefield parameters
> #include "toppar/charmm36.itp"
> #include "toppar/compound.itp"
> #include "toppar/DPPC.itp"
> #include "toppar/DPPE.itp"
> #include "toppar/TIP3.itp"
>
> [System]
> : Name
> Title
>
> [Molecules]
> : Compound #mols
> COMPOUND    72
> DPPE                230
> DPPC                26
> TIP3                  8960
>

Use grep to count unique atoms in each compound.  The simple fact is that either 
these numbers do not match what is in the coordinate file, or the contents of 
the .itp files are mangled in some way such that you get a different number of 
atoms than you're expecting.

-Justin

-- 
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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

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