Hi,
(I'm sending this to the list as well so others that may have the same
issue can see the resolution).
The 'nointramol' keyword specifically excludes intramolecular hydrogen
honds; all *intermolecular* hydrogen bonds are calculated. For your
first system (4hld-firstrun.prmtop) there are two solute molecules: a
protein beginning with SER and a ligand named 16T, so with
'nointramol' you will only get hydrogen bonds between the ligand and
solvent. For your second system
(GHEA-quercetagetin_01-secondrun.prmtop) you have three solute
molecules: two proteins beginning with ASP and a ligand named QTG, so
with 'nointramol' you get hydrogen bonds between both ASP and QTG as
well as ASP and ASP. If what you want is only the hydrogen bonds
between the proteins and the ligand you'll need two separate hydrogen
bond commands, one for each protein-ligand interaction, e.g.
hbond H1 :1-148,QTG nointramol ...
hbond H2 :149-296,QTG nointramol ...
Hope this helps,
-Dan
On Tue, Jan 24, 2017 at 11:42 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear Daniel,
> Thank you for your concern regarding my query. Amber archive is always very
> helpful for me and many other beginners so please do not say sorry.
> According to my observation, when my ligand name starts form digits like 13L
> or 16T then nointramol keyword extracts hydrogen bonding contacts between
> protein-residues and ligand only. While in my case, I named ligand QTG may
> be that is why nointramol keyword is not working. I figured this out by
> running cpptraj hydrogen script with nointramol keyword on three different
> simulation outputs. Ligand named in these simulation was 13L, 16T and QTG
> nointramol keyword just worked fine with those who have ligand named in
> digits. Please confirm my observations.
>
> Thanks
>
> Best Regards,
> Saman Yousuf Ali
>
>
>
> On Tuesday, January 24, 2017 6:43 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>
> Sorry for the delay on this. I haven't had a chance to look at your
> data before now.
>
> Cpptraj is working fine as far as I can tell; there is no problem with
> your output. I went through each line in both files and every pair has
> the acceptor in one molecule and the donor in a different molecule. If
> I missed something, please point it out.
>
> Let me know if you have more questions.
>
> -Dan
>
> On Wed, Jan 18, 2017 at 2:16 AM, Saman Yousuf ali
> <saman.yousufali64.yahoo.com> wrote:
>> Dear Daniel,
>> Thank you for the response. Please find the attached topology and hydrogen
>> bond analysis out files of both simulation.
>> I have serious concern about this issue. Kindly help me in this regard.
>>
>> Thanks in advance.
>>
>>
>>
>> On Monday, January 16, 2017 2:50 AM, Saman Yousuf ali
>> <saman.yousufali64.yahoo.com> wrote:
>>
>>
>> Dear All,
>> I have analyzed intermolecular hydrogen bonding of two different
>> simulation
>> trajectories via amber16 cpptraj, but got different results
>> Simulation1 production run input file
>> ===========================
>>
>> NPT production with no restrains
>> &cntrl
>> imin=0, ntx=7, irest=1, ntrx=1, ntxo=1,
>> ntpr=500, ntwx=500, ntwv=500, ntwe=500,
>> ntf=2, ntb=2, cut=8.0,
>> nsnb=100, igb=0,
>> nstlim=500000,
>> t=0.0, dt=0.002,
>> ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
>> vlimit=20,
>> ntp=1, taup=1.0, pres0=1.0, comp=44.6,
>> ntc=2, tol=0.00000001,
>> /
>> hbond.in
>> ========
>> trajin 4hld_prod1.mdcrd.gz
>> trajin 4hld_prod2.mdcrd.gz
>> trajin 4hld_prod3.mdcrd.gz
>> trajin 4hld_prod4.mdcrd.gz
>> trajin 4hld_prod5.mdcrd.gz
>> autoimage
>> strip :WAT
>> strip :Na+
>> hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat
>>
>> as a result of above pasted script, I just got ligand and residues
>> interactions.
>>
>> Run
>> ======
>>
>> CPPTRAJ: Trajectory Analysis. V16.12
>> ___ ___ ___ ___
>> | \/ | \/ | \/ |
>> _|_/\_|_/\_|_/\_|_
>>
>> | Date/time: 01/16/17 14:41:01
>> | Available memory: 150.184 MB
>>
>> Reading '../4hld.prmtop' as Amber Topology
>> INPUT: Reading input from 'h_bond.ptraj'
>> [trajin ../4hld_prod1.mdcrd.gz]
>> Reading '../4hld_prod1.mdcrd.gz' as Amber Trajectory
>> [trajin ../4hld_prod2.mdcrd.gz]
>> Reading '../4hld_prod2.mdcrd.gz' as Amber Trajectory
>> [trajin ../4hld_prod3.mdcrd.gz]
>> Reading '../4hld_prod3.mdcrd.gz' as Amber Trajectory
>> [trajin ../4hld_prod4.mdcrd.gz]
>> Reading '../4hld_prod4.mdcrd.gz' as Amber Trajectory
>> [trajin ../4hld_prod5.mdcrd.gz]
>> Reading '../4hld_prod5.mdcrd.gz' as Amber Trajectory
>> [autoimage]
>> AUTOIMAGE: To box center based on center of mass, anchor is first
>> molecule.
>> [strip :WAT]
>> STRIP: Stripping atoms in mask [:WAT]
>> [strip :Na+]
>> STRIP: Stripping atoms in mask [:Na+]
>> [hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat]
>> HBOND: Searching for Hbond donors/acceptors in region specified by *
>> Only looking for intermolecular hydrogen bonds.
>> Distance cutoff = 3.000, Angle Cutoff = 135.000
>> Writing # Hbond v time results to 4hld_hbond.agr
>> Writing Hbond avgs to 4hld_av_hbond.dat
>> ---------- RUN BEGIN -------------------------------------------------
>>
>>
>> Simulation2 production input file
>> ==========================
>> polyA-polyT 10-mer: 100ps MD
>> &cntrl
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 10.0, ntr = 0,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 500000, dt = 0.002,
>> ntpr = 1000, ntwx = 500, ntwr = 1000
>> /
>> hbond.in
>> ========
>> trajin md_simulation1.mdcrd.gz
>> trajin md_simulation2.mdcrd.gz
>> trajin md_simulation3.mdcrd.gz
>> trajin md_simulation4.mdcrd.gz
>> trajin md_simulation5.mdcrd.gz
>> trajin md_simulation6.mdcrd.gz
>> trajin md_simulation7.mdcrd.gz
>> trajin md_simulation8.mdcrd.gz
>> trajin md_simulation9.mdcrd.gz
>> trajin md_simulation10.mdcrd.gz
>> autoimage
>> strip :WAT
>> strip :Na+
>> hbond All nointramol out nhb.agr avgout avghb.dat
>>
>> Run
>> ========
>> CPPTRAJ: Trajectory Analysis. V16.12
>> ___ ___ ___ ___
>> | \/ | \/ | \/ |
>> _|_/\_|_/\_|_/\_|_
>>
>> | Date/time: 01/16/17 14:41:16
>> | Available memory: 8227.6 MB
>>
>> Reading 'GHEA-quercetagetin_01.prmtop' as Amber Topology
>> INPUT: Reading Input from file h_bond.ptraj
>> [trajin md_simulation1.mdcrd.gz]
>> Reading 'md_simulation1.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation2.mdcrd.gz]
>> Reading 'md_simulation2.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation3.mdcrd.gz]
>> Reading 'md_simulation3.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation4.mdcrd.gz]
>> Reading 'md_simulation4.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation5.mdcrd.gz]
>> Reading 'md_simulation5.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation6.mdcrd.gz]
>> Reading 'md_simulation6.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation7.mdcrd.gz]
>> Reading 'md_simulation7.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation8.mdcrd.gz]
>> Reading 'md_simulation8.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation9.mdcrd.gz]
>> Reading 'md_simulation9.mdcrd.gz' as Amber Trajectory
>> [trajin md_simulation10.mdcrd.gz]
>> Reading 'md_simulation10.mdcrd.gz' as Amber Trajectory
>> [autoimage]
>> AUTOIMAGE: To box center based on center of mass, anchor is first
>> molecule.
>> [strip :WAT]
>> STRIP: Stripping atoms in mask [:WAT]
>> [strip :Na+]
>> STRIP: Stripping atoms in mask [:Na+]
>> [hbond All nointramol out 4hld_hbond.agr avgout 4hld_av_hbond.dat]
>> HBOND: Searching for Hbond donors/acceptors in region specified by *
>> Only looking for intermolecular hydrogen bonds.
>> Distance cutoff = 3.000, Angle Cutoff = 135.000
>> Writing # Hbond v time results to 4hld_hbond.agr
>> Writing Hbond avgs to 4hld_av_hbond.dat
>>
>>
>> While for second one, I got both residue-residue and residue-ligand
>> interaction. Why results of both simulation hydrogen bond analysis are
>> different even I have used same system and script for running these
>> analysis. The first one results just ligand and residue interaction while
>> other one is printing both residue-residue and residue ligand hydrogen
>> bond.
>>
>> Where am I going wrong?
>> Thanks in advance for any suggestions.
>
>>
>>
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jan 25 2017 - 06:00:04 PST
