Hi Jason,
Thanks a lot for your reply.
I am using the following tleap script to add a bond between HEME and HIS.
loadamberparams frcmod.hemall
loadamberprep heme_all.in
addAtomTypes { { "DZ" "Zn" "sp3" } { "Zn" "Zn" "sp3" } }
loadOff znb.lib
loadOff hin.lib
loadOff hydroxide.lib
loadamberparams frcmod.zinc
fep = loadpdb clnFePPIX.pdb
bond fep.103.13 fep.181.1
addions fep Na+ 0
solvatebox fep TIP3PBOX 10.00 0.75
saveamberparm fep fep.prm.top fep.prm.crd
quit
The next thing I want to do would be to mimic the following restraints:
restrainAngle fep fep.103.14 fep.103.13 fep.181.1 20 124.0
restrainAngle fep fep.103.11 fep.103.13 fep.181.1 20 127.4
restrainAngle fep fep.103.13 fep.181.1 fep.181.2 20 93.1
restrainAngle fep fep.103.13 fep.181.1 fep.181.23 20 98.6
restrainAngle fep fep.103.13 fep.181.1 fep.181.39 20 106.6
restrainAngle fep fep.103.13 fep.181.1 fep.181.55 20 103.4
However, I am not sure how to use setangle to do this in the topology file
derived from the above tleap script as you have suggested.
It would be really helpful if you please direct me to some document/suggest me
how to go about doing this. If I start my MD with only the bond criterion, the
imidazole ring of HIS undergoes planar motion which I do not want.
Thanks again and I would look forward to hear from you.
Best Regards,
Moitrayee
> On Fri, Nov 15, 2013 at 6:59 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
>
>> Dear Amber Users,
>> I am planning to run an MD simulation with a pentacoordinated HEME-HIS. I
>> am
>> using the heme-all parameters (which is for coordinated sytem) and trying
>> to use
>> a patch from CHARMM to build in additional bonds, angles etc. and delete
>> some
>> angles using tleap.
>>
>> However, it seems that tleap has no function to add a new angle or delete
>> one. I
>> cn easily add a bond but not new angles, dihedrals. The patch is as
>> follows:
>> DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
>> BOND 1NE2 2FE
>> ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB
>> ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND
>>
>> When I translate this to tleap:
>>
>> fep = loadpdb fep.prm.pdb
>> delete angle fep.181.NA fep.181.FE fep.181.NC fep.181.NB fep.181.FE
>> fep.181.ND
>> bond fep.103.NE2 fep.181.FE
>> angle fep.103.CD2 fep.103.NE2 fep.181.FE fep.103.CE1 fep.103.NE2
>> fep.181.FE
>> fep.103.NE2 fep.181.FE fep.181.NA fep.103.NE2 fep.181.FE fep.181.NB
>> angle fep.103.NE2 fep.181.FE fep.181.NC fep.181.NE2 fep.181.FE
>> fep.181.ND
>>
>>
>> addions fep Na+ 0
>> solvatebox fep TIP3PBOX 10.00 0.75
>> saveamberparm fep fep.prm.top fep.prm.crd
>> quit
>>
>> However, there is no angle command in tleap. I am a little confused as to
>> how to
>> implement this. Any suggestion would be very much appreciated.
>>
>
> As Dave mentioned, there is no 'angle' command in tleap.
>
> You can create the topology file in tleap _without_ the angle parameters
> and then use the setAngle command in ParmEd to add the angles afterwards.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Nov 20 2013 - 19:00:03 PST
