[gmx-users] (no subject)

David spoel at xray.bmc.uu.se
Sun Aug 3 20:09:01 CEST 2003

On Sun, 2003-08-03 at 19:54, Jayant James Jayasundar wrote:
> hi all,
> I was just wondering how the protonation states of Histidines are 
> assigned by gromacs? For some histidines with low solvent 
> accessibility (found by means of WHATIF) the Histidines are 
> assigned a protonation state of HISB (accessibility is less than 
> 2.0) but for an accessibility of 24.9014 the histidine is assigned 
> a state HISB and for an accessibility of 19.305 the histidine is 
> assigned a state HISA then a histidine with accessibility 4.1372 
> the state assigned is HISH by gromacs  on what basis is the 
> assignments made as I am trying to do some pH based MD work??
First off all you can fully control protonation manually with the -inter
flag to pdb2gmx, and some more flags. Furthermore pdb2gmx computes the
hydrogen bonding pattern in the protein, and if there is indication that
the proton should be on the NE2 rather than ND1 it is put there.
Default  (in solution) is ND1. Doubly protonated is possible but depends
again on your hbonding pattern. If you  runpdb2gmx -debug the complete
list of hbonds will be dumped in pdb2gmx.log

> Regs
> Jayant
> Jayasundar Jayant James
> Research scholar
> Centre for Biotechnology
> Anna University. Chennai - 600 025.INDIA
> Ph 2350772(Office), Cell-9841042164,
> Res 4935864
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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