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-- ++++++++++++++++++++++++++++++++++++++++++++++++++ --- Francesco Pietra <chiendarret.gmail.com> schrieb am Do, 12.6.2008: > Von: Francesco Pietra <chiendarret.gmail.com> > Betreff: Re: AMBER: Combine mdcrd while stripping WAT problem > An: amber.scripps.edu > Datum: Donnerstag, 12. Juni 2008, 9:09 > Hi: > That is an excellent suggestion. Actually, I had already > tried that, > with both ambpdb and ambmask. Failure in both cases, > however. I just > describe here what happened with the first. Maybe someone > is > interested. > > $AMBERHOME/exe/ambpdb -p complex_pop_box.prmtop < > combined_production.mdcrd > combined_production.pdb > > New format PARM file being parsed > Version 1.000 Date 03/25/08 > forrtl: severe (64): input conversion error, unit -5, file > Internal > Formatted read > > To rule out that it was a problem of shortage of memory, I > run the > same for one of the production chunks. Exactly the same > error. > > Also, I tried with an initial prmtop/inpcrd combination for > both my > ligand and the protein, and both ambpdb and ambmask worked > correctly, > also in Amber10. I assume that mdcrd should behave as > inpcrd to this > respect. > > However, as the study at hand urged to be completed, > yesterday evening > I went to a debian linux machine with larger RAM. I > installed VMD and > could load all frames for the whole system of complex in > hydrated > membrane and box, performing clustering and getting fine > RMSD vs time > for both the protein and the ligand with plugins. Like I > did months > ago to circumvent a similar problem of getting matching > prmtop/mdcrd. > > That does not mean that I am not interested in getting a > workable > prmtop for a combined mdcrd for my systems. Either I was > not correctly > doing (which is the most likely possibility), or a program > to get > matching prmtop/mdcrd would be most useful. I understand > the problem > of convention, however. In fact, for the initial > preparation of my > systems, the part taken by Chimera was most troublesome. I > had to > rearrange atom names with four characters - and much more, > with great > help by Eric and Elaine - in order that leap could > understand them. > > Thanks > > francesco > > On Thu, Jun 12, 2008 at 7:59 AM, Alexander Metz > <alexander_metz2000.yahoo.de> wrote: > > Maybe you could create a working .prmtop file by: > > > > (1) creating a .pdb file with trajout and then > > (2) creating a new .prmtop file from this .pdb file > using LEaP > > > > Good luck, > > > > Alexander > > > > -- > > ++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > > > --- Francesco Pietra <chiendarret.gmail.com> > schrieb am Mi, 11.6.2008: > > > >> Von: Francesco Pietra > <chiendarret.gmail.com> > >> Betreff: Re: AMBER: Combine mdcrd while stripping > WAT problem > >> An: amber.scripps.edu > >> Datum: Mittwoch, 11. Juni 2008, 16:57 > >> Hi: > >> Still unsuccessful in loading cleanly the combined > >> (stripped) mdcrd > >> files to VMD. > >> Described here is what I did, should someone be so > patient > >> to check > >> for mistakes. > >> > >> I have a number of prmtop files, corresponding to > the > >> various steps. I > >> have now tried the two most naked ones, from > docking the > >> ligand onto > >> the protein with DOCK6.2. Here, a prmtop was for > flex > >> scoring, the > >> other one from amber score in implicit medium, > that is, WAT > >> only > >> appears in the prmtop as the last residue after > all protein > >> residues. > >> I deleted WAT from either one of these two prmtop > files and > >> tried with > >> VMD with the combined mdcrd, stripped of :WAT > :POP, and > >> nobox. Result: > >> highly distorted protein and ligand at each > snapshot. > >> > >> Surely there are other combinations of > mdcrd/prmtop. Those > >> I tried > >> (all other prmtop files - from embedding into the > lipidic > >> membrane - > >> contain WAT BOX and result from 'solvate box > model# > >> TIP3Box 12.0') led > >> to similarly distorted snapshots. I assume that I > missed > >> the right > >> choice of combinations. Before trying other ones, > it would > >> help to > >> appreciate where the above procedure is in error. > >> > >> Thanks a lot > >> francesco pietra > >> > >> On Tue, Jun 10, 2008 at 10:03 AM, Carlos > Simmerling > >> <carlos.simmerling.gmail.com> wrote: > >> > whether you say nobox depends on whether your > new > >> > stripped prmtop (and you must make one) has a > box or > >> > not. just be consistent and it should be ok. > >> > distortions come from the mdcrd and prmtop > not > >> > have the same amount of data per frame, > either > >> > from mismatch in natom or mismatch in box > presence. > >> > calros > >> > > >> > On Tue, Jun 10, 2008 at 3:37 AM, Francesco > Pietra > >> <chiendarret.gmail.com> wrote: > >> >> Hi: > >> >> Perhaps you also refer to discussion I > took part > >> to last year for the > >> >> same problem with Amber9. > >> >> > >> >> Like at that time, docking of the ligand > was now > >> carried out (DOCK6.2) > >> >> with the protein embodying a single > molecule of > >> water of > >> >> crystallization. That is, the prmtop > corresponding > >> to protein+ligand > >> >> before embedding into the membrane > contains that > >> WAT. I already tried > >> >> the WAT&POP stripped mdcrd with that > prmtop. > >> Did not work, i.e., both > >> >> the protein and the ligand looked like > heavily > >> distorted at each > >> >> snapshot when loading to VMD the stripped > mdcrd > >> file. > >> >> > >> >> I can try again with prmtop stripped > (with text > >> editor) of that WAT, > >> >> although as carried out above it did not > work. > >> Before doing that, a > >> >> question: is it meaningful to command > >> 'nobox' while stripping only WAT > >> >> (and not POP too)? > >> >> > >> >> Thanks for the suggestions. > >> >> francesco pietra > >> >> > >> >> On Sun, Jun 8, 2008 at 9:33 PM, Carlos > Simmerling > >> >> <carlos.simmerling.gmail.com> > wrote: > >> >>> also, if you strip water, you might > want to > >> use the "nobox" > >> >>> flag after trajout so that box > coordinate are > >> not written. by default > >> >>> they are. if you use the correct > prmtop > >> corresponding to the > >> >>> stripped system, try loading the > trajectory in > >> VMD using the > >> >>> coordinates with box and see if it > helps. > >> there is lots of > >> >>> discussion of this in the archives. > >> >>> > >> >>> On Sun, Jun 8, 2008 at 2:58 PM, > Gustavo Seabra > >> <gustavo.seabra.gmail.com> wrote: > >> >>>> On Sun, Jun 8, 2008 at 11:40 AM, > Francesco > >> Pietra <chiendarret.gmail.com> wrote: > >> >>>>> With Amber10, on accumulating > ns of > >> trajectory, I am facing a problem > >> >>>>> of trajectory analysis > unresolved > >> since Amber9 for the same protein > >> >>>>> and environment, though for a > >> different ligand. > >> >>>>> > >> >>>>> The system is a large > protein, > >> carrying a large non-peptidic ligand. > >> >>>>> It is embedded in a POP, > TIP3P > >> hydrated, membrane. Everything flows > >> >>>>> correctly, 39% faster with > pmemd with > >> respect to sander.MPI. > >> >>>>> > >> >>>>> What I am trying to do with > ptraj is > >> combining *.mdcrd while stripping WAT > >> >>>>> > >> >>>>> While a complete action would > be: > >> >>>>> > >> >>>>> trajin prod1.mdcrd.gz > >> >>>>> trajin prod2.mdcrd.gz > >> >>>>> ...................... > >> >>>>> trajout prod1-#_no_wat.mdcrd > nobox > >> >>>>> strip :WAT > >> >>>>> strip :POP > >> >>>>> > >> >>>>> I tried simply: > >> >>>>> > >> >>>>> trajin prod1.mdcrd.gz > >> >>>>> trajin prod2.mdcrd.gz > >> >>>>> ...................... > >> >>>>> trajout prod1-#_no_wat.mdcrd > >> >>>>> strip :WAT > >> >>>>> > >> >>>>> That in view of using the > *.prmtop for > >> MD and in order not to change > >> >>>>> the residue numbering. > >> >>>>> > >> >>>>> With the same *.prmtop used > for MD, > >> the combined file does not load > >> >>>>> cleanly with VMD. As > expected. > >> >>>> > >> >>>> What exaclty do you mean by > "not load > >> cleanly"? Do you get any error > >> >>>> messages? Anyways, I'm not > sure it > >> could ever load correctly, since > >> >>>> after stripping the waters the > number of > >> atoms in the prmtop file is > >> >>>> different than in the > prod1-#_no_wat.mdcrd > >> file. > >> >>>> > >> >>>>> I removed all WAT from > *.prmtop. The > >> same problem. > >> >>>> > >> >>>> I suppose there's more to it > than just > >> removing the "WAT" residues. > >> >>>> You may want to take a look into > the > >> 'rdparm' utility, described > >> >>>> together with ptraj. (Check the > >> "stripwater" and then > "writeparm" > >> >>>> commands). > >> >>>> > >> >>>> Gustavo. > >> >>>> > >> > ----------------------------------------------------------------------- > >> >>>> The AMBER Mail Reflector > >> >>>> To post, send mail to > amber.scripps.edu > >> >>>> To unsubscribe, send > "unsubscribe > >> amber" (in the *body* of the email) > >> >>>> to majordomo.scripps.edu > >> >>>> > >> >>> > >> >>> > >> >>> > >> >>> -- > >> >>> > >> > ----------------------------------------------------------------------- > >> >>> The AMBER Mail Reflector > >> >>> To post, send mail to > amber.scripps.edu > >> >>> To unsubscribe, send > "unsubscribe > >> amber" (in the *body* of the email) > >> >>> to majordomo.scripps.edu > >> >>> > >> >> > >> >> > >> >> > >> >> -- > >> >> Dr Francesco Pietra > >> >> Professor of Chemistry > >> >> Accademia Lucchese di Scienze, Lettere e > Arti, > >> founded in 1594 > >> >> Palazzo Ducale > >> >> 55100 Lucca (Italy) > >> >> > >> > ----------------------------------------------------------------------- > >> >> The AMBER Mail Reflector > >> >> To post, send mail to amber.scripps.edu > >> >> To unsubscribe, send "unsubscribe > amber" > >> (in the *body* of the email) > >> >> to majordomo.scripps.edu > >> >> > >> > > >> > ----------------------------------------------------------------------- > >> > The AMBER Mail Reflector > >> > To post, send mail to amber.scripps.edu > >> > To unsubscribe, send "unsubscribe > amber" (in > >> the *body* of the email) > >> > to majordomo.scripps.edu > >> > > >> > >> > >> > >> -- > >> Dr Francesco Pietra > >> Professor of Chemistry > >> Accademia Lucchese di Scienze, Lettere e Arti, > founded in > >> 1594 > >> Palazzo Ducale > >> 55100 Lucca (Italy) > >> > ----------------------------------------------------------------------- > >> The AMBER Mail Reflector > >> To post, send mail to amber.scripps.edu > >> To unsubscribe, send "unsubscribe amber" > (in the > >> *body* of the email) > >> to majordomo.scripps.edu > > > > > > > __________________________________________________________ > > Gesendet von Yahoo! Mail. > > Dem pfiffigeren Posteingang. > > http://de.overview.mail.yahoo.com > > > ----------------------------------------------------------------------- > > The AMBER Mail Reflector > > To post, send mail to amber.scripps.edu > > To unsubscribe, send "unsubscribe amber" (in > the *body* of the email) > > to majordomo.scripps.edu > > > > > > -- > Dr Francesco Pietra > Professor of Chemistry > Accademia Lucchese di Scienze, Lettere e Arti, founded in > 1594 > Palazzo Ducale > 55100 Lucca (Italy) > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" (in the > *body* of the email) > to majordomo.scripps.edu __________________________________________________________ Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang. http://de.overview.mail.yahoo.com ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Sun Jun 15 2008 - 06:07:28 PDT