[gmx-users] Regarding non zwitterionic structure to zwitterionic structure while using gmxpdb2gmx

[Mark Abraham]

Hi,

On Wed, Oct 18, 2017 at 12:05 PM Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Hello,
> I have a neutral glycine molecule [NH2CH2COOH] and if i give gmx pdb2gmx i
> m getting error as:-
> Fatal error:
> Atom HO in residue GLY 1 was not found in rtp entry GLY with 11 atoms
> while sorting atoms.
> For a hydrogen, this can be a different protonation state......
>
> So i use the -ignh flag (gmx pdb2gmx gly.pdb -o gly.gro -ignh) which gives
> me a zwitterionic structure and topology is created.(since i need to
> simulate in water, the zwitterionic structure is good.)
>
> 1] But if i convert the zwitterionic form of glycine into .mol2 format and
> upload to CGENFF server (i am using charmm FF) for creating the topology,
> the .str file that is generated shows a penalty of 99.5, which is not good.
>
> RESI glycin       0.000 ! param penalty=   0.100 ; charge penalty=  99.591
> GROUP            ! CHARGE   CH_PENALTY
> ATOM N      NG3P3  -0.336 !   32.195
> ATOM H1     HGP2    0.330 !    2.200
> ATOM H2     HGP2    0.330 !    2.200
> ATOM H3     HGP2    0.330 !    2.200
> ATOM CA     CG324   0.241 !   99.591
> ATOM HA1    HGA2    0.090 !    3.821
> ATOM HA2    HGA2    0.090 !    3.821
> ATOM C      CG2O3   0.445 !   98.841
> ATOM OT1    OG2D2  -0.760 !    8.256
> ATOM OT2    OG2D2  -0.760 !    8.256
>
> But if i compare the topology created by 'gmx pdb2gmx gly.pdb -o
> gly.gro -ignh' command then the charges of the atoms are different...
> then how is this possible..??
>

We don't know how the garbage charges got into the .mol2 file. Presumably
your conversion process didn't use the GROMACS topology as input, so the
issue is unrelated to GROMACS.


> Which topology is more reliable..??
>
> 2] if non zwitterionic form of glycine is given in form of .mol2, then
> the .str file give zero penalty.
>
> RESI *****        0.000 ! param penalty=   0.000 ; charge penalty=   0.000
> GROUP            ! CHARGE   CH_PENALTY
> ATOM N      NG321  -0.956 !    0.000
> ATOM CA     CG321   0.100 !    0.000
> ATOM C      CG2O2   0.751 !    0.000
> ATOM O      OG2D1  -0.551 !    0.000
> ATOM HA1    HGA2    0.090 !    0.000
> ATOM HA2    HGA2    0.090 !    0.000
> ATOM H      HGPAM2  0.338 !    0.000
> ATOM HN     HGPAM2  0.338 !    0.000
> ATOM OXT    OG311  -0.629 !    0.000
> ATOM HO     HGP1    0.429 !    0.000
>
> So which topology is more reliable for simulations..??
>

Which one models reality?

Mark


> Any suggestions ar appreciated..
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
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