[gmx-users] #include section in a .top file

[Justin Lemkul]

On 5/26/15 2:38 AM, soumadwip ghosh wrote:
> Ignore the previous incomplete mail.
>
> Dear GMX users,
>                            I am simulating some polyelectrolytes in the
> presence of a large organic cation. I have made both the .itp files from
> SWIISPARAM web server since I am using CHARMM27 force field. Next, I made
> the topology file for GROMACS like this-
>
>
>   GROMACS topology
> ;
> ; Include the force field
> #include "charmm27.ff/forcefield.itp"
> ; Define SWISSPARAM atomtypes here
> #include "atomtypes_nafion.itp"
> #include "atomtypes_tma.itp"
>
> ; Include chain topologies
> #include "sdg_nafion.itp"
> #include "tmaua.itp"
>
> ; Include water topology
> #include "charmm27.ff/tip3p.itp"
>
> ; Include generic ion topology
> #include "charmm27.ff/ions.itp"
>
> [ system ]
> Two proteins in water
>
> [ molecules ]
> LIG       1
> tma      37
> SOL         1750
> CL               36
>
> I have included atomtypes separately immediately after the force field
> description since previously issuing grompp was giving this error-------
>
> " fatal error
> '  [ atomtypes ]
> Invalid order for directive atomtypes'.
> Hence, I constructed the system.top file in the above way according to some
> relevant google discussion thread. My question is my .top file correct? the
> two .itp file are given below----
>
> The polyelectrolyte
> [ atomtypes ]
> ; name at.num  mass   charge  ptype    sigma            epsilon
> CR      6   12.0110  0.0  A         0.387541    0.230120
> F       9   18.9984  0.0  A         0.290433    0.564840
> OR      8   15.9994  0.0  A         0.315378    0.636386
> SO2    16   32.0660  0.0  A         0.374177    1.966480
> O2CM    8   15.9994  0.0  A         0.302905    0.502080
>
>
> [ pairtypes ]
> ;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
> INTERACTIONS
> CR       CR     1      0.338541    0.041840
> CR       F      1      0.314487    0.153730
> CR       OR     1      0.326960    0.163176
> CR       SO2    1      0.356359    0.286841
> CR       O2CM   1      0.320723    0.144938
>
>
> The cation
> [ atomtypes ]
> ; name at.num  mass   charge  ptype    sigma            epsilon
> CR      6   12.0110  0.0  A         0.387541    0.230120
> NRP     7   14.0067  0.0  A         0.329632    0.836800
> HCMM    1    1.0079  0.0  A         0.235197    0.092048
>
>
> [ pairtypes ]
> ;  i     j    func     sigma1-4       epsilon1-4 ; THESE ARE 1-4
> INTERACTIONS
> CR       CR     1      0.338541    0.041840
> CR       NRP    1      0.334087    0.187114
> CR       HCMM   1      0.286869    0.062059
>
> Then when I proceeded for grompp there was a warning that-
>
> 'atomtype CR has been overridden'
>
> I guess this is not surprising since both the itp's contain this CR atom.
> So, I started doing grompp with maxwarn 1 command and it seems everything
> works fina.
>
> My question is have I done everything correctly and whether the redundancy
> of CR atoms will be problematic later on or not.

Just don't get in the habit of doing this.  Here, it's innocuous, but you can 
have very bad unintended consequences if you make this general practice.  The 
best practice is to clean up your inputs and avoid duplication.

>
> If the construction of my .top file is ok, can anyone suggest me a way by
> which I can avoid this 'atomtype CR has been overridden' thsi warning?
>

Don't be redundant :)

-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

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