Hello,
Thank you for your email. I am currently out of office and have limited access to my emails.
I will review your message following my return.
Best regards,
Marie Brut
Le 22 juil. 2022 à 21:45, Marie Brut via AMBER <amber.ambermd.org> a écrit :
> Hello,
>
> Thank you for your email. I am currently out of office and have limited access to my emails.
> I will review your message following my return.
>
> Best regards,
>
> Marie Brut
>
> Le 22 juil. 2022 à 21:45, Marie Brut via AMBER <amber.ambermd.org> a écrit :
>
> Hello,
>
> Thank you for your email. I am currently out of office and have limited access to my emails.
> I will review your message following my return.
>
> Best regards,
>
> Marie Brut
>
> Le 22 juil. 2022 à 21:44, Marie Brut via AMBER <amber.ambermd.org> a écrit :
>
> Hello,
>
> Thank you for your email. I am currently out of office and have limited access to my emails.
> I will review your message following my return.
>
> Best regards,
>
> Marie Brut
>
> Le 22 juil. 2022 à 21:41, Daniel Roe via AMBER <amber.ambermd.org> a écrit :
>
> OK - I've checked the first few frames and as far as I can tell
> cpptraj and vmd are giving the same results for # hbonds calcd (I
> modified your cpptraj script to give the number of hydrogen bonds vs
> time via 'out numhbvtime.dat'):
>
> $ head HBA100Kvmdhbonds.dat
> 0 386
> 1 381
> 2 370
> 3 362
> 4 345
> 5 371
> 6 365
> 7 372
> 8 355
> 9 362
> $ awk '{print $1 "\t" $2;}' numhbvtime.dat
> #Frame 100K[UU]
> 1 386
> 2 381
> 3 370
> 4 361
> 5 345
> 6 371
> 7 365
> 8 372
> 9 355
> 10 362
>
> I also note you're writing out the average solvent-solute hbonds and
> bridging info, but not the average solute-solute hbonds (easily
> accomplished by adding 'avgout hbavg.dat').
>
> As far as I can tell, both programs are producing equivalent results.
> I'm guessing any differences you see is in how VMD groups the data
> into the details (HBA100KvmdDetails.dat) file. The VMD code makes no
> distinction between hydrogens, while cpptraj does. For example, if you
> grab all the Lys 108 data out of the VMD file you get things like:
>
> $ grep LYS108 HBA100KvmdDetails.dat
> LYS108-Side-NZ ASP340-Side-OD2 33.28%
> SER337-Main-N LYS108-Main-O 32.17%
> LYS108-Side-NZ GLU104-Main-O 0.39%
> LYS108-Side-NZ LYS91-Main-O 0.89%
> LYS108-Side-NZ SER103-Main-O 0.17%
>
> Whereas if you grab the Lys 108 data from cpptraj output you get:
>
> $ grep LYS_108 hbavg.dat
> LYS_108.O SER_337.H SER_337.N 579 0.3217
> 2.8196 163.1371
> ASP_340.OD2 LYS_108.HZ2 LYS_108.NZ 206 0.1144
> 2.7326 166.1036
> ASP_340.OD2 LYS_108.HZ3 LYS_108.NZ 205 0.1139
> 2.7263 166.3880
> ASP_340.OD2 LYS_108.HZ1 LYS_108.NZ 188 0.1044
> 2.7293 165.7254
> LYS_91.O LYS_108.HZ3 LYS_108.NZ 6 0.0033
> 2.9093 165.3931
> LYS_91.O LYS_108.HZ2 LYS_108.NZ 5 0.0028
> 2.9101 163.7331
> LYS_91.O LYS_108.HZ1 LYS_108.NZ 5 0.0028
> 2.9107 167.9775
> GLU_104.O LYS_108.HZ1 LYS_108.NZ 4 0.0022
> 2.7859 161.7393
> GLU_104.O LYS_108.HZ3 LYS_108.NZ 2 0.0011
> 2.7666 160.9960
> GLU_104.O LYS_108.HZ2 LYS_108.NZ 1 0.0006
> 2.7385 166.7346
> SER_103.O LYS_108.HZ3 LYS_108.NZ 1 0.0006
> 2.7500 161.4854
> SER_103.O LYS_108.HZ2 LYS_108.NZ 1 0.0006
> 2.8366 162.1290
> SER_103.O LYS_108.HZ1 LYS_108.NZ 1 0.0006
> 2.9242 160.6470
>
> Note that when there is only 1 hydrogen the results between the 2
> codes are equivalent, but cpptraj breaks up the data per-hydrogen
> while VMD does not. So it's just a difference in how the frames are
> counted.
>
> Hopefully this clears things up.
>
> -Dan
>
> On Fri, Jul 22, 2022 at 2:06 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> It gave me an "Error downloading" before but seems to be working now,
> so the problem was likely a transient one on my end.
>
> -Dan
>
> On Fri, Jul 22, 2022 at 12:34 PM Matthew Guberman-Pfeffer
> <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Hi Dan, The link still works for me. Can you please let me know if it doesn’t work for you. What’s the message you see?
> Best,
> Matthew
>
> On Jul 22, 2022, at 10:18 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> I don't think I got to the link in time. Any chance you can send a new
> one? Thanks,
>
> -Dan
>
> On Thu, Jul 7, 2022 at 4:13 PM Matthew Guberman-Pfeffer
> <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Hi Dan, I’m now looking at the details of the H-bonds instead of the total number, and I—to the best of my knowledge—see a difference between the output for H-bond analysis in Vmd and CPPTRAJ after setting the criteria to be equivalent. Below is a dropbox link to a directory with a ReadMe.txt file that explains what everything is and how I am comparing the outputs.
>
> Dropbox link: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fsh%2Fghiwb6r4qqsl0k0%2FAAC-ZEARN3nQF-_HDtjKTU8ma%3Fdl%3D0&data=05%7C01%7C%7C2ecf8ecf5c3846922db108da6bed04f5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637940962970768008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pxrdTUD3aM%2FzQ0c3UILgDjzg%2FiXUkRw4zpGLM0c329w%3D&reserved=0
>
> Basically, I see that some H-bonds (all with an occupancy less than 10% but one as high as 7%) are found by VMD and not CPPTRAJ. I’m not saying either program is right/wrong; I only want to understand the origin of the difference.
>
> Best,
> Matthew
>
>
> On Jul 7, 2022, at 12:24 PM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Dan, for you and others on the list, I want to revise my original post: If the angle and distance criteria are set to 160° and 3 Å, respectively, CPPTRAJ gives exactly the same H-bond count as VMD. I was mistaken before because I looked at the total number of H-bonds given by CPPTRAJ and the total number of unique H-bonds found by VMD. The first of these is on a per-frame basis, the latter is over the entire trajectory, which is why I thought VMD was finding many more H-bonds.
>
> Best,
> Matthew
>
>
> On Jun 24, 2022, at 3:36 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
> *Message sent from a system outside of UConn.*
>
>
> Both cpptraj and vmd use simple geometric criteria - as long as the criteria match the results should be the same. Please send me off list a topology and coordinates so I can reproduce. Please also send the exact cpptraj input.
>
> On Fri, Jun 24, 2022 at 3:13 PM Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Hi Dan,
>
> Yes, I noticed that CPPTRAJ and VMD use different definitions of the angles. I just worked in the reverse direction. I changed the angle in CPPTRAJ to be > 160° to match the VMD definition of < 20°. I think you were suggesting to change the VMD default to <45° to match the CPPTRAJ default of >135°.
>
> Using <20° in VMD and >160° in CPPTRAJ, I see a huge difference in the number of H-bonds (<300 by CPPTRAJ and almost 3000 by VMD). VMD also counts a huge number of H-bonds with water, whereas CPPTRAJ only reports a few hundred. Is something else besides the angle definition, which I think I already addressed, going on? Should I send you files so you can look at the comparison?
>
> Best,
> Matthew
>
>
> On Jun 24, 2022, at 2:51 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> On Mon, Jun 20, 2022 at 8:23 AM Matthew Guberman-Pfeffer via AMBER
> <amber.ambermd.org> wrote:
>
> I’m trying to understand why the number is so small. If I run the H-bond analysis in VMD, I find ~2000 unique H-bonds. (I made sure to adjust the distance and angle criteria in CPPTRAJ and VMD to be the same for this comparison.)
>
> Make sure that the angle cutoff in particular is the same; cpptraj and
> VMD defines the cutoffs differently. A valid hydrogen bond for cpptraj
> has a D-H-A angle greater than the cutoff (default 135). In VMD it's
> *deviation* from linear (180 deg.), so the cpptraj default of 135 is
> 45 for VMD.
>
> Does that make sense?
>
> -Dan
>
>
> Any insight would be much appreciated.
>
> Best,
> Matthew
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C2ecf8ecf5c3846922db108da6bed04f5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637940962970768008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hC7Ax1186qTCiJgR168aoAjzC84%2Bg32TBcpOrl7bObI%3D&reserved=0
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:36:33 PDT
