[gmx-users] ATB topology: itp to top conversion

[Justin Lemkul]

On 6/13/17 7:06 PM, Anna Lappala wrote:
> Dear all,
> 
> I am confused: I have my pdb file as well as the itp file produced by ATB. I want to convert these into top and gro files but the molecule is not recognised by the forcefield when I do the following:
> 
> pdb2gmx -f input.pdb -o output.gro -i topology.itp
> 
> I have looked through tutorials and on the mailing list, but mostly the workaround is to #include the itp file into an existing top file - which i do not have because i only have a heteromolecule, and no protein...
> 

The purpose of pdb2gmx is to write a topology.  You already have that.  The .itp 
format (typically the topology of a single entity) is hardly different from that 
of a .top (which is a system topology).  A .top file:

1. #includes or otherwise has parameters from a parent force field
2. Has a [system] directive
3. Has a [molecules] directive

Your topology from ATB is based on a GROMOS force field parameter set, which is 
probably already in GROMACS and you can therefore start your .top with a 
suitable #include statement to that parent force field.  Then #include your 
.itp, add [system] and [molecules], and you have a functional .top file.

As for format conversion, use editconf, not pdb2gmx.  But you don't have to use 
.gro (a common misconception).

-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

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