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-- Dr. Charo I. del Genio Senior Lecturer in Statistical Physics Applied Mathematics Research Centre (AMRC) Design Hub Coventry University Technology Park Coventry CV1 5FB UK https://charodelgenio.weebly.com ------------------------------ Message: 3 Date: Mon, 9 Nov 2020 12:41:40 +0900 From: Prathit Chatterjee <prathit.biophysics.gmail.com> Subject: Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system To: carlos.simmerling.gmail.com, ross.cgl.ucsf.edu Cc: amber.ambermd.org Message-ID: <CAH3AqM5KpXVD-g8nch13ZDk3-r4R_o_6v8nv-fXCUd-EXAwG8A.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Prof. Simmerling and Dr. Ross, Sorry to reply to you back from the embedded amber digest, I did not receive separate reply emails. The precision of numbers is the same in both cases, and the format is .crd, please see below: *This is for the original amber coordinates*: parm prot.top trajin /homes/epsilon/users/diem/project_t-ab/traj_1/production/crd/ *T_310K_1_md001.crd* 1 10 #centering strip :WAT strip :Na+ strip :Cl- center :1-43 mass origin image origin center familiar pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out -------------- *This is for the protein only generated coordinates*: parm prot.top trajin /homes/epsilon/users/pchatterjee/vmd_anal_prep/diem_1/ *T_310K_prot_diem_1_100ns.crd* 1 10 pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out ------------- Also, *I generated the protein-only amber coordinates as follows in VMD*: mol new /homes/epsilon/users/diem/project_t-ab/traj_10/production/whole.top type parm7 mol addfile /homes/epsilon/users/diem/project_t-ab/traj_10/production/crd/T_310K_10_md$n .crd *type netcdf* waitfor all set frames [molinfo top get numframes] set nf [expr {[molinfo top get numframes]-1}] set a [atomselect top protein] animate *write crdbox* diem_10/PHF43_310K_prot_$f.crd beg 0 end $nf waitfor all sel $a I tried to write the protein only coordinates in several ways until reaching the above mentioned procedure, loading the original coordinates as netcdf, and writing the final protein only coordinates as crdbox. Likewise, the coordinates for visualizing the original and protein-only coordinates could be visualized properly without any apparent unnatural bonds. Best Regards, Prathit On Sun, Nov 8, 2020 at 5:00 AM <amber-request.ambermd.org> wrote: > > Message: 3 > Date: Sat, 7 Nov 2020 05:28:00 -0800 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] Discrepancy between interaction energy of amber > coordinate trajectories of a system > To: amber.ambermd.org > Message-ID: <d455da94-5267-c71a-ed48-56c1e16ef604.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > I wonder if the precision of the numbers is the same in both cases? What > format is your mdcrd in? If ASCII, precision is much reduced, otherwise > less of an issue but worth checking by e.g. calcing yourself with the > operations in a different order. > > Bill > > ------------------------------ > > Message: 4 > Date: Sat, 7 Nov 2020 09:44:44 -0500 > From: Carlos Simmerling <carlos.simmerling.gmail.com> > Subject: Re: [AMBER] Discrepancy between interaction energy of amber > coordinate trajectories of a system > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAGk3s-QY5CtFHALO95DVCN6kzcMmi-ePv4SjzxN= > 9pXo3vX1Mw.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > You haven't said much about how you actually did these steps, but I can > imagine that making a new (protein trajectory in ascii format with limited > precision could lead to small changes in coordinates and energy > differences. > > On Sat, Nov 7, 2020, 8:19 AM Prathit Chatterjee < > prathit.biophysics.gmail.com> wrote: > > > Dear AMBER experts, > > > > I had compiled a protein only amber trajectory of an explicitly solvated > > simulation with VMD, which I was able to visualize properly and run > certain > > analyses with it in VMD as well. > > > > But, for cross-checking, I tried to calculate the pairwise interaction of > > the protein only generated trajectory (with VMD), and the original AMBER > > coordinates. > > > > The results, although very similar, are showing certain discrepancy as > > follows: > > > > [pchatterjee.node51 pairwise_IE]$ tail -f test*/pairwise_IE.out > > *==> test1/pairwise_IE.out <== [THIS IS THE ORIGINAL AMBER COORDINATE]* > > 1 -186.3642 -2973.0974 > > 2 -189.9812 -2966.1259 > > 3 -199.5370 -2957.7041 > > 4 -196.3846 -2983.7931 > > 5 -197.8264 -2981.1530 > > 6 -184.0711 -2971.6430 > > 7 -194.3659 -2970.1477 > > 8 -189.0441 -2956.9308 > > 9 -197.0864 -2948.2561 > > 10 -196.4939 -3010.1367 > > > > *==> test2/pairwise_IE.out <==[THIS IS THE PROTEIN ONLY GENERATED AMBER > > COORIDNATE IN VMD]* > > 1 -186.3943 -2972.9815 > > 2 -189.9798 -2966.1573 > > 3 -199.5455 -2957.6502 > > 4 -196.3961 -2983.7881 > > 5 -197.8009 -2981.1609 > > 6 -184.0410 -2971.7176 > > 7 -194.3681 -2970.0830 > > 8 -189.0185 -2956.9181 > > 9 -197.1040 -2948.2302 > > 10 -196.4685 -3010.0947 > > > > Although the global picture will be the same with such minor > discrepancy, I > > just want to know for the sake of knowing what the underlying reason > could > > be. > > > > Any comments/suggestions will be extremely helpful. > > > > Thank you in advance, > > Best Regards, > > Prathit > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ Message: 4 Date: Mon, 9 Nov 2020 04:57:21 +0000 From: MADHUSMITA DEVI <madhusmi.iitg.ac.in> Subject: [AMBER] Addition of polyatomic ions in Leap To: "amber.ambermd.org" <amber.ambermd.org> Message-ID: <BM1PR0101MB13953242683CC5AC946A71C8EEEA0.BM1PR0101MB1395.INDPRD01.PROD.OUTL OOK.COM> Content-Type: text/plain; charset="iso-8859-1" Dear Amber Users, I would like to know if the addions/ addions2 command in leap work for salts having a polyatomic anion. Thank you in advance. With regards, Madhusmita Devi ------------------------------ Message: 5 Date: Mon, 9 Nov 2020 07:20:57 +0000 From: Raman Preet Singh <ramanpreetsingh.hotmail.com> Subject: Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX To: AMBER Mailing List <amber.ambermd.org> Message-ID: <BMXPR01MB3526A6890793349B6DD7E884B3EA0.BMXPR01MB3526.INDPRD01.PROD.OUTLOOK. COM> Content-Type: text/plain; charset="iso-8859-1" We have two workstations with octa core Ryzen processors. One workstation has a single NVIDIA GPU while the second has 3 NVIDIA GPUs. They seemed to work very well initially (8 CPU Ryzen cores + 1 GPU performance was higher than a 32 cores of Xeon E5 v2 processor processor for NAMD) but after a few months started hanging and showing a decrease in performance (but still better than 32 core Xeon E5 v2). This is the issue with both workstations after around 6-10 months. We often run simulations for several days at a stretch as required for typical MD simulations. I typically use Amber tools for analysis and Gromacs or NAMD for MD as we don't have Amber license. Since you are looking at a relatively higher end processor family (Threadripper), things might work well. But do look at reviews on major online stores or post on Quora or Tom's. I have read reviews where AMD processors show problems due to heating but those not frequent reviews as people are content with low cost of AMD processors. Regards, Raman Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Jordi Bujons <jordi.bujons.iqac.csic.es> Sent: Sunday, November 8, 2020 11:50:17 PM To: amber.ambermd.org <amber.ambermd.org> Subject: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Hi, At our group we are considering buying a new machine equipped with one or two 3080 or 3090 GPUs to run Amber 20. The computer store recommends to get an AMD based computer, with a Ryzen 3960X CPU and a TRX40 motherboard that supports the PCIe 4.0 bus present in Nvidia 3080/3090. I have seen several comments on the list about the 3080 and 3090 GPUs, but does anybody has experience with such a combination of CPU+GPU? Will Amber 20 take much advantage of having PCIe 4.0 rather than PCIe 3.0? Any comments will be appreciated. Jordi ---------------------------------------------------------------------------- ---------- Jordi Bujons, PhD Dept. of Biological Chemistry (QB) Institute of Advanced Chemistry of Catalonia (IQAC) National Research Council of Spain (CSIC) Address: Jordi Girona 18-26, 08034 Barcelona, Spain Phone: <tel:%2B34%20934006100%20ext.%201291> +34 934006100 ext. 1291 FAX: <tel:%2B34%20932045904> +34 932045904 <mailto:jordi.bujons.iqac.csic.es> jordi.bujons.iqac.csic.es <http://www.iqac.csic.es> http://www.iqac.csic.es -- El software de antivirus Avast ha analizado este correo electr?nico en busca de virus. https://www.avast.com/antivirus _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 6 Date: Mon, 9 Nov 2020 08:40:53 +0000 From: Gustaf Olsson <gustaf.olsson.lnu.se> Subject: Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor To: AMBER Mailing List <amber.ambermd.org> Message-ID: <505BE789-5FE8-425E-8147-259BE9251F4C.lnu.se> Content-Type: text/plain; charset="utf-8" Setting the debug level > 1 did produce a promising start: HBOND: Searching for Hbond donors/acceptors in region specified by * Distance cutoff = 3.000, Angle Cutoff = 135.000 The printout from running the analysis with no additional input produces a list of "Acceptor-only atoms? and "Donor/acceptor sites?. This is roughly what I was looking for. I can solve this with some awk/grep combination though what I was hoping for was the same output on a ?per resname? basis. My test system had 100 carboxylic acid molecules and water. I get 100 entries for the "carbonyl oxygen" and another 100 for the ?hydroxyl group?. I was hoping to get entries on a ?residue name/type? basis ?on XXX found these acceptors/donors, on YYY, on ZZZ?. Don?t know if this is of any greater interest to anyone else and should most likely not be considered a priority issue. Thank you for you reply and suggestion Best regards // Gustaf > On 6 Nov 2020, at 14:53, Daniel Roe <daniel.r.roe.gmail.com> wrote: > > Hi, > > On Fri, Nov 6, 2020 at 4:25 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote: >> I was curious regarding the definition of hbond donors/acceptors in cpptraj. From what I understand, cpptraj allows a relatively loose definition of these and is capable of of some degree of auto-detection. > > As stated in the manual, a hydrogen bond in the hbond command is > defined as being between an acceptor heavy atom A, a donor hydrogen > atom H, and a donor heavy atom D. If the A to D distance is less than > the distance cutoff (default 3 Ang) and the A-H-D angle is greater > than the angle cutoff (default 135 deg.) a hydrogen bond is considered > formed. Both cutoffs can be adjusted by the user. > >> >> If my understanding is correct, is it possible to run cpptraj in a way, potentially just using the prmtop/inpcrd files, to print out all identified donors/acceptors? > > You can do this by setting the actions debug level to something > greater than 1 (so put e.g. 'debug actions 1' before the 'hbond' > command) and running on 1 frame. Maybe that should be a keyword > option... > > -Dan > >> >> Best regards >> // Gustaf >> _______________________________________________ >> 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 ------------------------------ Message: 7 Date: Mon, 9 Nov 2020 08:45:26 +0000 From: Gustaf Olsson <gustaf.olsson.lnu.se> Subject: Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor To: AMBER Mailing List <amber.ambermd.org> Message-ID: <D31EFFB4-EC96-4DB0-8992-5F612E1652C9.lnu.se> Content-Type: text/plain; charset="utf-8" Oh, one more thing which popped up, is there a keyword to include water in the analyses without needing to specify it as being a donor/acceptor (having it included with the ?auto-detection? results). Best regards Gustaf > On 9 Nov 2020, at 09:40, Gustaf Olsson <gustaf.olsson.lnu.se> wrote: > > Setting the debug level > 1 did produce a promising start: > > HBOND: Searching for Hbond donors/acceptors in region specified by * > Distance cutoff = 3.000, Angle Cutoff = 135.000 > > The printout from running the analysis with no additional input produces a list of "Acceptor-only atoms? and "Donor/acceptor sites?. This is roughly what I was looking for. I can solve this with some awk/grep combination though what I was hoping for was the same output on a ?per resname? basis. My test system had 100 carboxylic acid molecules and water. I get 100 entries for the "carbonyl oxygen" and another 100 for the ?hydroxyl group?. I was hoping to get entries on a ?residue name/type? basis ?on XXX found these acceptors/donors, on YYY, on ZZZ?. > > Don?t know if this is of any greater interest to anyone else and should most likely not be considered a priority issue. > > Thank you for you reply and suggestion > Best regards > // Gustaf > > >> On 6 Nov 2020, at 14:53, Daniel Roe <daniel.r.roe.gmail.com> wrote: >> >> Hi, >> >> On Fri, Nov 6, 2020 at 4:25 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote: >>> I was curious regarding the definition of hbond donors/acceptors in cpptraj. From what I understand, cpptraj allows a relatively loose definition of these and is capable of of some degree of auto-detection. >> >> As stated in the manual, a hydrogen bond in the hbond command is >> defined as being between an acceptor heavy atom A, a donor hydrogen >> atom H, and a donor heavy atom D. If the A to D distance is less than >> the distance cutoff (default 3 Ang) and the A-H-D angle is greater >> than the angle cutoff (default 135 deg.) a hydrogen bond is considered >> formed. Both cutoffs can be adjusted by the user. >> >>> >>> If my understanding is correct, is it possible to run cpptraj in a way, potentially just using the prmtop/inpcrd files, to print out all identified donors/acceptors? >> >> You can do this by setting the actions debug level to something >> greater than 1 (so put e.g. 'debug actions 1' before the 'hbond' >> command) and running on 1 frame. Maybe that should be a keyword >> option... >> >> -Dan >> >>> >>> Best regards >>> // Gustaf >>> _______________________________________________ >>> 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 > ------------------------------ Message: 8 Date: Mon, 09 Nov 2020 09:52:22 +0100 From: "MYRIAN TORRES RICO" <myriam.torres.iiq.csic.es> Subject: Re: [AMBER] protein domain "broken" To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20201109095222.Horde.3dcsiRNCqxW_snCZsTvl6ml.webmail.csic.es> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes Hi Anselm, I'm bearing in mind your answers, thanks you so much. I found that the disulphide bond was broken in the docking process, and hence I didn't defined in my simulation. Regards Myriam "Dr. Anselm Horn" <anselm.horn.fau.de> escribi?: > Hi Myriam, > > just to sum up: > Your first problem was that you forgot to define the disulfide bond, and > thus your simulation ran with two cystein residues lacking that bond. > => You have to re-run your simulations. > > Your second problem is that your system shows a change in secondary > structure during the course of simulation. This is by no means strange, > but reflects the ability of MD simulations to describe the system - but > can also be an artifact due to the forcefield used. > > Good examples for peptide systems exhibiting a change in secondary > structure are simulations describiting ab-initio folding of peptides. > > Also be aware that your visualization program normally decides according > to the backbone angle topology, what secondary structure the system is > depicted in. So, small changes here might change the style. > > > Regards > > Anselm > > > On 11/06/2020 01:39 PM, MYRIAN TORRES RICO wrote: >> >> Hi Carlos, >> >> >> Sorry, I'm not explaining myself well, my problem is one of two >> sheets has lost the structure... and it >> had not happened to me until now. Can a molecular dynamic cause this >> phenomenon in protein? lose the structure of one of the sheets? >> >> Thanks in advance >> >> >> Myriam >> >> >> Carlos Simmerling <carlos.simmerling.gmail.com> escribi?: >> >>> Did you define the disulfide bond specifically in leap with a bond command >>> when you built your system? >>> >>> On Fri, Nov 6, 2020, 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote: >>> >>>> Hi Myriam, >>>> >>>> I'm sorry but I do not understand your second problem: >>>> One of the domains in your protein has "disappeared"? What do you mean >>>> by that? >>>> In your screenshots, I can spot a single protein chain with two (more or >>>> less structured) regions and a ligand system in sticks, but nothing >>>> "disappeared" here. The structure of sheet structure on the left side is >>>> lost in one pic, but the protein is still there... >>>> >>>> Regards >>>> >>>> Anselm >>>> >>>> >>>> On 11/06/2020 12:21 PM, MYRIAN TORRES RICO wrote: >>>>> Hi Bill, >>>>> >>>>> I rectify with my previous message, sorry. I have checked just that, >>>>> and indeed my disulfide bond was not defined, and that's why it >>>>> appeared broken in all dynamics. So my problem is summarized in: Even >>>>> not having put this bond in my input ... because in some cases one of >>>>> the two domains of the protein disappears? I am attaching two images >>>>> so you can see it better. I have opened the final molecule with >>>>> several programs and only one of two domains appears... >>>>> >>>>> Thanks in advance, >>>>> >>>>> >>>>> Myriam >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Bill Ross <ross.cgl.ucsf.edu> escribi?: >>>>> >>>>>> Normally bonds that seem to disappear were not made in the first place. >>>>>> >>>>>> Bill >>>>>> >>>>>> >>>>>> On 11/6/20 2:45 AM, MYRIAN TORRES RICO wrote: >>>>>>> Dear all, >>>>>>> >>>>>>> I wanted to take a query about some results that I have obtained in my >>>>>>> molecular dynamics. >>>>>>> I have launched a dynamic of a protein-ligand complex (the ligand is a >>>>>>> tretasaccharide), and of the two domains that the pdb of my protein >>>>>>> initially presents, the disulfide bonds that form one of them ends up >>>>>>> breaking ... But the energy data endings are the same as in any other >>>>>>> dynamic that has been launched under the same conditions and with the >>>>>>> same complex ... >>>>>>> Has someone this or something similar happened to him? >>>>>>> any ideas? >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> Myriam >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> AMBER mailing list >>>>>>> AMBER.ambermd.org >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> -- >>>>>> Phobrain.com >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 9 Date: Mon, 9 Nov 2020 14:23:57 +0530 From: koushik kasavajhala <koushik.sbiiit.gmail.com> Subject: Re: [AMBER] protein domain "broken" To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAKFWzuV_PHMd8w0oOoYjbLebe0qpmL+_VtoA67m8i5nbUcxNvw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Mon, Nov 9, 2020 at 2:22 PM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es> wrote: > Hi Anselm, > > I'm bearing in mind your answers, thanks you so much. I found that the > disulphide bond was broken in the docking process, and hence I didn't > defined in my simulation. > > > Regards > > Myriam > > "Dr. Anselm Horn" <anselm.horn.fau.de> escribi?: > > > Hi Myriam, > > > > just to sum up: > > Your first problem was that you forgot to define the disulfide bond, and > > thus your simulation ran with two cystein residues lacking that bond. > > => You have to re-run your simulations. > > > > Your second problem is that your system shows a change in secondary > > structure during the course of simulation. This is by no means strange, > > but reflects the ability of MD simulations to describe the system - but > > can also be an artifact due to the forcefield used. > > > > Good examples for peptide systems exhibiting a change in secondary > > structure are simulations describiting ab-initio folding of peptides. > > > > Also be aware that your visualization program normally decides according > > to the backbone angle topology, what secondary structure the system is > > depicted in. So, small changes here might change the style. > > > > > > Regards > > > > Anselm > > > > > > On 11/06/2020 01:39 PM, MYRIAN TORRES RICO wrote: > >> > >> Hi Carlos, > >> > >> > >> Sorry, I'm not explaining myself well, my problem is one of two > >> sheets has lost the structure... and it > >> had not happened to me until now. Can a molecular dynamic cause this > >> phenomenon in protein? lose the structure of one of the sheets? > >> > >> Thanks in advance > >> > >> > >> Myriam > >> > >> > >> Carlos Simmerling <carlos.simmerling.gmail.com> escribi?: > >> > >>> Did you define the disulfide bond specifically in leap with a bond > command > >>> when you built your system? > >>> > >>> On Fri, Nov 6, 2020, 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> > wrote: > >>> > >>>> Hi Myriam, > >>>> > >>>> I'm sorry but I do not understand your second problem: > >>>> One of the domains in your protein has "disappeared"? What do you mean > >>>> by that? > >>>> In your screenshots, I can spot a single protein chain with two (more > or > >>>> less structured) regions and a ligand system in sticks, but nothing > >>>> "disappeared" here. The structure of sheet structure on the left side > is > >>>> lost in one pic, but the protein is still there... > >>>> > >>>> Regards > >>>> > >>>> Anselm > >>>> > >>>> > >>>> On 11/06/2020 12:21 PM, MYRIAN TORRES RICO wrote: > >>>>> Hi Bill, > >>>>> > >>>>> I rectify with my previous message, sorry. I have checked just that, > >>>>> and indeed my disulfide bond was not defined, and that's why it > >>>>> appeared broken in all dynamics. So my problem is summarized in: Even > >>>>> not having put this bond in my input ... because in some cases one of > >>>>> the two domains of the protein disappears? I am attaching two images > >>>>> so you can see it better. I have opened the final molecule with > >>>>> several programs and only one of two domains appears... > >>>>> > >>>>> Thanks in advance, > >>>>> > >>>>> > >>>>> Myriam > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Bill Ross <ross.cgl.ucsf.edu> escribi?: > >>>>> > >>>>>> Normally bonds that seem to disappear were not made in the first > place. > >>>>>> > >>>>>> Bill > >>>>>> > >>>>>> > >>>>>> On 11/6/20 2:45 AM, MYRIAN TORRES RICO wrote: > >>>>>>> Dear all, > >>>>>>> > >>>>>>> I wanted to take a query about some results that I have obtained > in my > >>>>>>> molecular dynamics. > >>>>>>> I have launched a dynamic of a protein-ligand complex (the ligand > is a > >>>>>>> tretasaccharide), and of the two domains that the pdb of my protein > >>>>>>> initially presents, the disulfide bonds that form one of them ends > up > >>>>>>> breaking ... But the energy data endings are the same as in any > other > >>>>>>> dynamic that has been launched under the same conditions and with > the > >>>>>>> same complex ... > >>>>>>> Has someone this or something similar happened to him? > >>>>>>> any ideas? > >>>>>>> > >>>>>>> Thanks in advance, > >>>>>>> > >>>>>>> Myriam > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> AMBER mailing list > >>>>>>> AMBER.ambermd.org > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>> -- > >>>>>> Phobrain.com > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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 > >> > > > > > > _______________________________________________ > > 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 > ------------------------------ Message: 10 Date: Mon, 9 Nov 2020 14:29:00 +0530 From: koushik kasavajhala <koushik.sbiiit.gmail.com> Subject: Re: [AMBER] protein domain "broken"m To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAKFWzuXrOv7Xww+mMCJG9KVLyrDbfbzZAurdAoHH+AbKk1WFvA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Mon, Nov 9, 2020 at 2:22 PM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es> wrote: > Hi Anselm, > > I'm bearing in mind your answers, thanks you so much. I found that the > disulphide bond was broken in the docking process, and hence I didn't > defined in my simulation. > > > Regards > > Myriam > > "Dr. Anselm Horn" <anselm.horn.fau.de> escribi?: > > > Hi Myriam, > > > > just to sum up: > > Your first problem was that you forgot to define the disulfide bond, and > > thus your simulation ran with two cystein residues lacking that bond. > > => You have to re-run your simulations. > > > > Your second problem is that your system shows a change in secondary > > structure during the course of simulation. This is by no means strange, > > but reflects the ability of MD simulations to describe the system - but > > can also be an artifact due to the forcefield used. > > > > Good examples for peptide systems exhibiting a change in secondary > > structure are simulations describiting ab-initio folding of peptides. > > > > Also be aware that your visualization program normally decides according > > to the backbone angle topology, what secondary structure the system is > > depicted in. So, small changes here might change the style. > > > > > > Regards > > > > Anselm > > > > > > On 11/06/2020 01:39 PM, MYRIAN TORRES RICO wrote: > >> > >> Hi Carlos, > >> > >> > >> Sorry, I'm not explaining myself well, my problem is one of two > >> sheets has lost the structure... and it > >> had not happened to me until now. Can a molecular dynamic cause this > >> phenomenon in protein? lose the structure of one of the sheets? > >> > >> Thanks in advance > >> > >> > >> Myriam > >> > >> > >> Carlos Simmerling <carlos.simmerling.gmail.com> escribi?: > >> > >>> Did you define the disulfide bond specifically in leap with a bond > command > >>> when you built your system? > >>> > >>> On Fri, Nov 6, 2020, 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> > wrote: > >>> > >>>> Hi Myriam, > >>>> > >>>> I'm sorry but I do not understand your second problem: > >>>> One of the domains in your protein has "disappeared"? What do you mean > >>>> by that? > >>>> In your screenshots, I can spot a single protein chain with two (more > or > >>>> less structured) regions and a ligand system in sticks, but nothing > >>>> "disappeared" here. The structure of sheet structure on the left side > is > >>>> lost in one pic, but the protein is still there... > >>>> > >>>> Regards > >>>> > >>>> Anselm > >>>> > >>>> > >>>> On 11/06/2020 12:21 PM, MYRIAN TORRES RICO wrote: > >>>>> Hi Bill, > >>>>> > >>>>> I rectify with my previous message, sorry. I have checked just that, > >>>>> and indeed my disulfide bond was not defined, and that's why it > >>>>> appeared broken in all dynamics. So my problem is summarized in: Even > >>>>> not having put this bond in my input ... because in some cases one of > >>>>> the two domains of the protein disappears? I am attaching two images > >>>>> so you can see it better. I have opened the final molecule with > >>>>> several programs and only one of two domains appears... > >>>>> > >>>>> Thanks in advance, > >>>>> > >>>>> > >>>>> Myriam > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Bill Ross <ross.cgl.ucsf.edu> escribi?: > >>>>> > >>>>>> Normally bonds that seem to disappear were not made in the first > place. > >>>>>> > >>>>>> Bill > >>>>>> > >>>>>> > >>>>>> On 11/6/20 2:45 AM, MYRIAN TORRES RICO wrote: > >>>>>>> Dear all, > >>>>>>> > >>>>>>> I wanted to take a query about some results that I have obtained > in my > >>>>>>> molecular dynamics. > >>>>>>> I have launched a dynamic of a protein-ligand complex (the ligand > is a > >>>>>>> tretasaccharide), and of the two domains that the pdb of my protein > >>>>>>> initially presents, the disulfide bonds that form one of them ends > up > >>>>>>> breaking ... But the energy data endings are the same as in any > other > >>>>>>> dynamic that has been launched under the same conditions and with > the > >>>>>>> same complex ... > >>>>>>> Has someone this or something similar happened to him? > >>>>>>> any ideas? > >>>>>>> > >>>>>>> Thanks in advance, > >>>>>>> > >>>>>>> Myriam > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> AMBER mailing list > >>>>>>> AMBER.ambermd.org > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>> -- > >>>>>> Phobrain.com > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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 > >> > > > > > > _______________________________________________ > > 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 > ------------------------------ Message: 11 Date: Mon, 9 Nov 2020 14:30:20 +0530 From: koushik kasavajhala <koushik.sbiiit.gmail.com> Subject: Re: [AMBER] protein domain "broken" To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAKFWzuUn4AjJLHPsYMg9cqd7iujcB7QAB9tsqH+2D3gFn0wK6g.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Mon, Nov 9, 2020 at 2:22 PM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es> wrote: > Hi Anselm, > > I'm bearing in mind your answers, thanks you so much. I found that the > disulphide bond was broken in the docking process, and hence I didn't > defined in my simulation. > > > Regards > > Myriam > > "Dr. Anselm Horn" <anselm.horn.fau.de> escribi?: > > > Hi Myriam, > > > > just to sum up: > > Your first problem was that you forgot to define the disulfide bond, and > > thus your simulation ran with two cystein residues lacking that bond. > > => You have to re-run your simulations. > > > > Your second problem is that your system shows a change in secondary > > structure during the course of simulation. This is by no means strange, > > but reflects the ability of MD simulations to describe the system - but > > can also be an artifact due to the forcefield used. > > > > Good examples for peptide systems exhibiting a change in secondary > > structure are simulations describiting ab-initio folding of peptides. > > > > Also be aware that your visualization program normally decides according > > to the backbone angle topology, what secondary structure the system is > > depicted in. So, small changes here might change the style. > > > > > > Regards > > > > Anselm > > > > > > On 11/06/2020 01:39 PM, MYRIAN TORRES RICO wrote: > >> > >> Hi Carlos, > >> > >> > >> Sorry, I'm not explaining myself well, my problem is one of two > >> sheets has lost the structure... and it > >> had not happened to me until now. Can a molecular dynamic cause this > >> phenomenon in protein? lose the structure of one of the sheets? > >> > >> Thanks in advance > >> > >> > >> Myriam > >> > >> > >> Carlos Simmerling <carlos.simmerling.gmail.com> escribi?: > >> > >>> Did you define the disulfide bond specifically in leap with a bond > command > >>> when you built your system? > >>> > >>> On Fri, Nov 6, 2020, 6:50 AM Dr. Anselm Horn <anselm.horn.fau.de> > wrote: > >>> > >>>> Hi Myriam, > >>>> > >>>> I'm sorry but I do not understand your second problem: > >>>> One of the domains in your protein has "disappeared"? What do you mean > >>>> by that? > >>>> In your screenshots, I can spot a single protein chain with two (more > or > >>>> less structured) regions and a ligand system in sticks, but nothing > >>>> "disappeared" here. The structure of sheet structure on the left side > is > >>>> lost in one pic, but the protein is still there... > >>>> > >>>> Regards > >>>> > >>>> Anselm > >>>> > >>>> > >>>> On 11/06/2020 12:21 PM, MYRIAN TORRES RICO wrote: > >>>>> Hi Bill, > >>>>> > >>>>> I rectify with my previous message, sorry. I have checked just that, > >>>>> and indeed my disulfide bond was not defined, and that's why it > >>>>> appeared broken in all dynamics. So my problem is summarized in: Even > >>>>> not having put this bond in my input ... because in some cases one of > >>>>> the two domains of the protein disappears? I am attaching two images > >>>>> so you can see it better. I have opened the final molecule with > >>>>> several programs and only one of two domains appears... > >>>>> > >>>>> Thanks in advance, > >>>>> > >>>>> > >>>>> Myriam > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> Bill Ross <ross.cgl.ucsf.edu> escribi?: > >>>>> > >>>>>> Normally bonds that seem to disappear were not made in the first > place. > >>>>>> > >>>>>> Bill > >>>>>> > >>>>>> > >>>>>> On 11/6/20 2:45 AM, MYRIAN TORRES RICO wrote: > >>>>>>> Dear all, > >>>>>>> > >>>>>>> I wanted to take a query about some results that I have obtained > in my > >>>>>>> molecular dynamics. > >>>>>>> I have launched a dynamic of a protein-ligand complex (the ligand > is a > >>>>>>> tretasaccharide), and of the two domains that the pdb of my protein > >>>>>>> initially presents, the disulfide bonds that form one of them ends > up > >>>>>>> breaking ... But the energy data endings are the same as in any > other > >>>>>>> dynamic that has been launched under the same conditions and with > the > >>>>>>> same complex ... > >>>>>>> Has someone this or something similar happened to him? > >>>>>>> any ideas? > >>>>>>> > >>>>>>> Thanks in advance, > >>>>>>> > >>>>>>> Myriam > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> AMBER mailing list > >>>>>>> AMBER.ambermd.org > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>> -- > >>>>>> Phobrain.com > >>>>>> > >>>>>> _______________________________________________ > >>>>>> 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 > >> > > > > > > _______________________________________________ > > 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 > ------------------------------ Message: 12 Date: Mon, 9 Nov 2020 08:40:09 -0500 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Addition of polyatomic ions in Leap To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20201109134009.lys5oo2cvpcqvsnu.Davids-MBP.fios-router.home> Content-Type: text/plain; charset=us-ascii; format=flowed On Mon, Nov 09, 2020, MADHUSMITA DEVI wrote: > >I would like to know if the addions/ addions2 command in leap work for >salts having a polyatomic anion. Have you tried this? I would suggest adding ions before adding waters, since a polyatomic ion would displace more than one water molecule. Alternatives are packmol and AddToBox. ....dac ------------------------------ Message: 13 Date: Mon, 9 Nov 2020 09:51:55 -0500 From: Carlos Simmerling <carlos.simmerling.gmail.com> Subject: Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system To: AMBER Mailing List <amber.ambermd.org> Cc: Prathit Chatterjee <prathit.biophysics.gmail.com> Message-ID: <CAGk3s-Q_e5=WYhBS5uufG0bA=n9U+FfXjSknPZ0HPNh0Ruf1yw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" I cannot comment on what VMD may have changed in the coordinates, but with limited precision in ASCII crd files it would be expected that things like the image and center commands that move atoms would produce slightly different values for things like interatomic distances. Using binary netcdf files is likely to reduce this problem. On Sun, Nov 8, 2020 at 10:41 PM Prathit Chatterjee < prathit.biophysics.gmail.com> wrote: > Dear Prof. Simmerling and Dr. Ross, > > Sorry to reply to you back from the embedded amber digest, I did not > receive separate reply emails. > > The precision of numbers is the same in both cases, and the format is > .crd, please see below: > > *This is for the original amber coordinates*: > parm prot.top > trajin /homes/epsilon/users/diem/project_t-ab/traj_1/production/crd/ > *T_310K_1_md001.crd* 1 10 > > #centering > strip :WAT > strip :Na+ > strip :Cl- > > center :1-43 mass origin > image origin center familiar > > pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 > vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out > -------------- > > *This is for the protein only generated coordinates*: > parm prot.top > trajin /homes/epsilon/users/pchatterjee/vmd_anal_prep/diem_1/ > *T_310K_prot_diem_1_100ns.crd* 1 10 > > pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 > vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out > ------------- > > Also, *I generated the protein-only amber coordinates as follows in VMD*: > > mol new > /homes/epsilon/users/diem/project_t-ab/traj_10/production/whole.top type > parm7 > mol addfile > /homes/epsilon/users/diem/project_t-ab/traj_10/production/crd/T_310K_10_md$n .crd > *type netcdf* waitfor all > > set frames [molinfo top get numframes] > set nf [expr {[molinfo top get numframes]-1}] > > set a [atomselect top protein] > animate *write crdbox* diem_10/PHF43_310K_prot_$f.crd beg 0 end > $nf waitfor all sel $a > > I tried to write the protein only coordinates in several ways until > reaching the above mentioned procedure, loading the original coordinates as > netcdf, and writing the final protein only coordinates as crdbox. > Likewise, the coordinates for visualizing the original and protein-only > coordinates could be visualized properly without any apparent unnatural > bonds. > > Best Regards, > Prathit > > > On Sun, Nov 8, 2020 at 5:00 AM <amber-request.ambermd.org> wrote: > >> >> Message: 3 >> Date: Sat, 7 Nov 2020 05:28:00 -0800 >> From: Bill Ross <ross.cgl.ucsf.edu> >> Subject: Re: [AMBER] Discrepancy between interaction energy of amber >> coordinate trajectories of a system >> To: amber.ambermd.org >> Message-ID: <d455da94-5267-c71a-ed48-56c1e16ef604.cgl.ucsf.edu> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> I wonder if the precision of the numbers is the same in both cases? What >> format is your mdcrd in? If ASCII, precision is much reduced, otherwise >> less of an issue but worth checking by e.g. calcing yourself with the >> operations in a different order. >> >> Bill >> >> ------------------------------ >> >> Message: 4 >> Date: Sat, 7 Nov 2020 09:44:44 -0500 >> From: Carlos Simmerling <carlos.simmerling.gmail.com> >> Subject: Re: [AMBER] Discrepancy between interaction energy of amber >> coordinate trajectories of a system >> To: AMBER Mailing List <amber.ambermd.org> >> Message-ID: >> <CAGk3s-QY5CtFHALO95DVCN6kzcMmi-ePv4SjzxN= >> 9pXo3vX1Mw.mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> You haven't said much about how you actually did these steps, but I can >> imagine that making a new (protein trajectory in ascii format with limited >> precision could lead to small changes in coordinates and energy >> differences. >> >> On Sat, Nov 7, 2020, 8:19 AM Prathit Chatterjee < >> prathit.biophysics.gmail.com> wrote: >> >> > Dear AMBER experts, >> > >> > I had compiled a protein only amber trajectory of an explicitly solvated >> > simulation with VMD, which I was able to visualize properly and run >> certain >> > analyses with it in VMD as well. >> > >> > But, for cross-checking, I tried to calculate the pairwise interaction >> of >> > the protein only generated trajectory (with VMD), and the original AMBER >> > coordinates. >> > >> > The results, although very similar, are showing certain discrepancy as >> > follows: >> > >> > [pchatterjee.node51 pairwise_IE]$ tail -f test*/pairwise_IE.out >> > *==> test1/pairwise_IE.out <== [THIS IS THE ORIGINAL AMBER COORDINATE]* >> > 1 -186.3642 -2973.0974 >> > 2 -189.9812 -2966.1259 >> > 3 -199.5370 -2957.7041 >> > 4 -196.3846 -2983.7931 >> > 5 -197.8264 -2981.1530 >> > 6 -184.0711 -2971.6430 >> > 7 -194.3659 -2970.1477 >> > 8 -189.0441 -2956.9308 >> > 9 -197.0864 -2948.2561 >> > 10 -196.4939 -3010.1367 >> > >> > *==> test2/pairwise_IE.out <==[THIS IS THE PROTEIN ONLY GENERATED AMBER >> > COORIDNATE IN VMD]* >> > 1 -186.3943 -2972.9815 >> > 2 -189.9798 -2966.1573 >> > 3 -199.5455 -2957.6502 >> > 4 -196.3961 -2983.7881 >> > 5 -197.8009 -2981.1609 >> > 6 -184.0410 -2971.7176 >> > 7 -194.3681 -2970.0830 >> > 8 -189.0185 -2956.9181 >> > 9 -197.1040 -2948.2302 >> > 10 -196.4685 -3010.0947 >> > >> > Although the global picture will be the same with such minor >> discrepancy, I >> > just want to know for the sake of knowing what the underlying reason >> could >> > be. >> > >> > Any comments/suggestions will be extremely helpful. >> > >> > Thank you in advance, >> > Best Regards, >> > Prathit >> > _______________________________________________ >> > AMBER mailing list >> > AMBER.ambermd.org >> > http://lists.ambermd.org/mailman/listinfo/amber >> > >> >> ------------------------------ Message: 14 Date: Mon, 9 Nov 2020 06:54:22 -0800 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Addition of polyatomic ions in Leap To: amber.ambermd.org Message-ID: <3ba21195-1a77-f457-ece3-239f13feab52.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed If orientation matters, I'd find another way. 3-5 atoms and special attention to equilibration might be easier to plow through, but packmol sounds like a better solution in general based on name and reputation, and may be worth learning in the long run. Bill On 11/8/20 8:57 PM, MADHUSMITA DEVI wrote: > Dear Amber Users, > > I would like to know if the addions/ addions2 command in leap work for salts having a polyatomic anion. > > Thank you in advance. > > With regards, > Madhusmita Devi > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- Phobrain.com ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 3178, Issue 1 ************************************** -- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 11 2020 - 06:00:05 PST