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

[Dilip H N]

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..??

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..??

Any suggestions ar appreciated..

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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