[gmx-users] How to proceed with molecule.itp file

[Justin Lemkul]

On 5/21/15 8:00 AM, Sotirios Dionysios I. Papadatos wrote:
> Hi,
> This indeed begins to clarify things but just to make sure I got it right.
> I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule.
> So I use the pdb2gmx to the molecule, I edit the topol.top that is produced (even in error a .top file is produced) and then I replace everything from the .itp file that I made.?
> Then I continue with the grompp command?

Don't use pdb2gmx at all.  You said you have an .itp file; this is already 
pretty much a .top as there are only small differences (.top is for a system, 
.itp is for a molecule, but in your case it sounds like molecule = system).

See http://www.gromacs.org/Documentation/File_Formats/.itp_File

The .top itself is as easy (if not easier) than the example already provided.

Just do the following in a text editor to create a .top:
1. #include a parent force field (unless the .itp specifies all the parameters 
explicitly)
2. #include the molecule.itp file
3. Add a [system] directive with some name
4. Add a [molecules] directive that tells grompp there is 1 of your molecule

That's all there is to it.

-Justin

> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Cara Kreck <cara.kreck at student.curtin.edu.au>
> Sent: Thursday, May 21, 2015 1:59 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] How to proceed with molecule.itp file
>
> Hi Sotirios,
>
> You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids.
>
> If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the protein to use with pdb2gmx. I would then recommend you remove all the .top specific parts of this file and convert it to a .itp file for just the protein. Then make your own .top file using the bits you removed and link everything together. Alternatively you can just add to the include and molecule sections at the end of pdb2gmx's .top file.
>
> If you don't have any protein, don't bother with pdb2gmx at all.
>
> Here's an example DIY .top file:
>
> ; Forcefield files
> #include "gromos53a6.ff/forcefield.itp"
> #include "./lipids_vdw.itp"
>
> ; Parameter set for DOPC
> #include "./dopc.itp"
>
> ; Include DMSO topology
> #include "./dmso.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> [ system ]
> ; Name
> 128 DOPC in DMSO solution
>
> [ molecules ]
> ; name     number
> DOPC          128
> DMSO          496
> SOL          7573
>
>
> Make sure you use the molecule names defined in your .itp files and list the molecules in the same order that they appear in your coordinate file.
>
> Hope that helps,
>
> Cara
>
>
>> From: si.papadatos at edu.cut.ac.cy
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Date: Thu, 21 May 2015 07:13:00 +0000
>> Subject: [gmx-users] How to proceed with molecule.itp file
>>
>> Hi,
>>
>> I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.
>>
>> My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp.
>>
>> Please help
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>
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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

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