VMD-L Mailing List

From: amin_at_imtech.res.in
Date: Tue Nov 06 2012 - 22:18:43 CST

Thanks a lot for the suggestions. Would it be better to make a box large enough
to have the protein or a small box and then replicate it to make a bigger one. I
had thought of using charmm for sucrose with the following patch:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!PATCHES for the pyranose-furanose mixed di/polysaccharides !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

PRES SUCR 0.00 ! pram; make sucrose, apply to AGLC,BFRU
dele atom 1HO1
dele atom 2O2
dele atom 2HO2
GROU
ATOM 1C1 CC3162 0.29 !
ATOM 1O1 OC302 -0.36 !
ATOM 2C2 CC3051 0.38 !
ATOM 1H1 HCA1 0.09 !
ATOM 1C5 CC3163 0.11 !
ATOM 1H5 HCA1 0.09 !
ATOM 1O5 OC3C61 -0.40 !
ATOM 2O5 OC3C51 -0.40 !
ATOM 2C5 CC3153 0.11 !
ATOM 2H5 HCA1 0.09 !
BOND 1O1 2C2
! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL)
IC 1O5 1C1 1O1 2C2 1.4300 108.97 106.13 115.17 1.4632
IC 1C1 1O1 2C2 2O5 1.4159 115.17 -47.60 114.57 1.3880
IC 1O1 2C2 2O5 2C5 1.4632 114.57 -100.55 109.86 1.4233
IC 2O5 1O1 *2C2 2C1 1.3880 114.57 121.04 106.87 1.5052

Can I please have some help on how to apply this patch to all the sucrose
molecules in the solvent box?

Warm Regards.
Amin.

> Hi,
>
> Create the boxes, equilibrate them for a bit, then insert your protein and
> remove the overlapping solvent molecules. The membrane protein
> tutorial<http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf>shows
> how to remove the lipids that overlap the protein. I'm sure it would
> be easy to adapt for solvent molecules. Perhaps somebody has an easier way,
> this is just off the top of my head:)
>
> Best regards,
> Ajasja
>
> On 6 November 2012 18:01, <amin_at_imtech.res.in> wrote:
>
>> Dear all,
>> I want to solvate my protein with water and sucrose at a defined
>> concentration
>> eg 30% sucrose solution. Can someone please guide me how to do this? While
>> trying few things, I have made some boxes having different number of water
>> and
>> sucrose molecules with packmol but have little idea on how to proceed. Any
>> suggestions would be appreciated.
>> Regards.
>> Amin.
>>
>> ______________________________________________________________________
>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
>> पिन कोड/PIN CODE :160036
>> दूरभाष/EPABX :0172 6665 201-202
>>
>

______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202