[gmx-users] histidine (HISB) planarity >> how about Trp?
siu at bioinformatik.uni-saarland.de
Mon Aug 14 18:07:13 CEST 2006
I am also trying G53a6 in my protein simulation and it is observed that
TRP is less planar as compared to those in OPLS. The angle distribution
of the impropers are calculated to be wider and thus less populated in
the equilibrium angle. Would this hint to a problem in the setup or ff?
Berk Hess wrote:
>> From: Anthony Armstrong <armstron at queen.med.jhmi.edu>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] histidine (HISB) planarity
>> Date: Fri, 11 Aug 2006 17:19:24 -0400 (EDT)
>> I was having problems keeping my histidines planar, and had to manually
>> edit the .top file produced by pdb2gmx in order to fix the problem.
>> I was
>> just wondering if this problem (i.e. incorrect and incomplete improper
>> dihedral records in the top file) is isolated to histidine topologies
>> generated by pdb2gmx using the G53a6 ff parameters or if manual
>> intervention is frequently required for such standard geometries. I'm
>> using Gromacs v3.3. I start with a pdb file of an extended
>> peptide (with planar his) and issue:
>> pdb2gmx -f -ignh -inter 1STN.pdb -o 1STN.gro -p 1STN.top -ff G53a6
>> whereupon I specify the single histidine to be of type HISB. After:
>> To correct this it was necessary to delete:
>> 32 35 30 33 2 gi_1
>> (this auto generated improper was largely responsible for the ring
>> puckering - its removal alone caused much of the problem to be
>> and to add:
>> 34 30 35 33 2 gi_1
>> (which brough the HE2 hydrogen slightly out of plain back into plain)
> Indeed this is incorrect.
> Atom number 32 in the improper dihedral should be replaced by 34.
> The error is caused by a mistake in ffG53a5/6.rtp fro HISB, the line:
> CE1 ND1 NE2 HD2 gi_1
> should be:
> CE1 ND1 NE2 HE1 gi_1
> I have corrected this for the next release.
>> Is it recommended that I look over every record in the topology
>> file? Is
>> this necessary? Thanks.
> Well, it is always recommended to check to whole topology, as one can
> never exclude errors. However, for a reasonable sized protein this
> is a nearly impossible task.
> The hope is that when the force field files, in this case the building
> files, do not change too often and too much and when thousands of users
> use them (like with Gromacs), errors will be found quickly and files
> be reliable.
> In this case the error stems for the original GROMOS building block file
> we have used for making the Gromacs rtp files. The previous GROMOS
> 43 and 45 force fields did not have explicit hydrogens on the carbons
> in the ring and apparently the improper for one of the new hydrogens
> was typed incorrectly.
> All other interactions for all histidine types seem to be correct.
> Thanks for reporting this error,
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