[gmx-users] topology file construction

[Justin Lemkul]

On 3/19/17 10:02 AM, abhisek Mondal wrote:
> Hi,
>
>     I'm using following topology configuration for the above said
> heteroatom:
>
>      1        OM     1  ANP     O1G     1   -0.348  15.9994
>      2         P     1  ANP PG     1    0.971  30.9738
>      3        OM     1  ANP     O2G     1   -0.348  15.9994
>      4        OM     1  ANP     O3G     1   -0.348  15.9994
>      5        NL     1  ANP     N3B     1   -0.275  14.0067
>      6         H     1  ANP     H3B     1    0.398   1.0080
>      7         P     1  ANP PB     2    0.971  30.9738
>      8        OM     1  ANP     O1B     2   -0.348  15.9994
>      9        OM     1  ANP     O2B     2   -0.348  15.9994
>     10        OA     1  ANP     O3A     3   -0.348  15.9994
>     11         P     1  ANP PA     3    0.971  30.9738
>     12        OM     1  ANP     O1A     3   -0.348  15.9994
>     13        OM     1  ANP     O2A     3   -0.348  15.9994
>     14        OA     1  ANP     O5'     3   -0.348  15.9994 ;'
>     15       CH2     1  ANP     C5'     4    0.000  14.0270 ;'
>     16       CH1     1  ANP     C4'     4    0.000  13.0190 ;'
>     17        OA     1  ANP     O4'     4   -0.348  15.9994 ;'
>     18       CH1     1  ANP     C3'     5    0.000  13.0190 ;'
>     19        OA     1  ANP     O3'     5   -0.348  15.9994 ;'
>     20         H     1  ANP     H8L     5    0.398   1.0080
>     21       CH1     1  ANP     C2'     5    0.000  13.0190 ;'
>     22        OA     1  ANP     O2'     5   -0.348  15.9994 ;'
>     23         H     1  ANP     H8M     5    0.398   1.0080
>     24       CH1     1  ANP     C1'     5    0.000  13.0190 ;'
>     25        NR     1  ANP N9     6   -0.275  14.0067
>     26       CR1     1  ANP C8     6   -0.100  12.0110
>     27        HC     1  ANP H8     6    0.100   1.0080
>     28        NR     1  ANP N7     6   -0.275  14.0067
>     29         C     1  ANP C5     6    0.150  12.0110
>     30         C     1  ANP C4     7    0.150  12.0110
>     31        NR     1  ANP N3     7   -0.275  14.0067
>     32       CR1     1  ANP C2     7   -0.100  12.0110
>     33        HC     1  ANP H2     7    0.100   1.0080
>     34        NR     1  ANP N1     7   -0.275  14.0067
>     35         C     1  ANP C6     7    0.150  12.0110
>     36        NT     1  ANP N6     7   -0.275  14.0067
>     37         H     1  ANP     H62     7    0.398   1.0080
>     38         H     1  ANP     H61     7    0.398   1.0080
>
> But even after I neutralize the charge using:
>
> *grompp_mpi -f em.mdp -c solv.gro -p topol.top -o ions.tpr*
> *genion_mpi -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> -neutral -conc 0.1*
>
> It says the following when I ran *grompp_mpi -f nvt.mdp -c em.gro -p
> topol.top -n index.ndx -o nvt.tpr* :
> NOTE 1 [file topol.top, line 10075]:
>   System has non-zero total charge: -0.472999
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
> Can you please help me out here ? Although the equilibration is running but
> is it alright to go with it ?
>

Is it possible for any molecule to acquire 0.472999 of an electron?  Clearly the 
answer is no, so the topology is badly broken and any simulation you do is 
invalid.  Garbage in, garbage out :)

You shouldn't try to parametrize this whole molecule at once; most force fields 
already have ATP in them, and this is just a phosphoramide analog of it, so you 
have most of the parameters that you need.  I would also not choose GROMOS, as 
it is not widely used for nucleic acid/nucleotide simulations.  CHARMM or AMBER 
are better choices.  You need to focus on parametrizing the phosphoramide 
linkage (charges and bonded parameters), not the whole thing.  PRODRG isn't even 
going to get you close with the dihedral parameters because there's nothing 
similar in the GROMOS force field upon which to base those parameters, AFAIK.

-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

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