From a283212@lrzpc10174.lrz-muenchen.de Fri Jan 23 03:16:53 1998 Received: from sunsrv5.lrz-muenchen.de for a283212@lrzpc10174.lrz-muenchen.de by www.ccl.net (8.8.3/950822.1) id CAA26740; Fri, 23 Jan 1998 02:53:43 -0500 (EST) Received: from lrzpc10174.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Fri, 23 Jan 98 08:53:39 +0100 Received: by lrzpc10174.lrz-muenchen.de (NX5.67e/NX3.0S) id AA00857; Fri, 23 Jan 98 08:53:38 +0100 Message-Id: <9801230753.AA00857@lrzpc10174.lrz-muenchen.de> Mime-Version: 1.0 (NeXT Mail 3.3 v118.2) Content-Type: multipart/alternative; boundary=NeXT-Mail-801923790-14 Content-Transfer-Encoding: 7bit X-Image-Url: ftp://ftp.imo.physik.uni-muenchen.de/pub/Images/heller.tiff X-Face: #K8+M!=vK|\bQ[&P:z)d$Q:i(@36P1!7if~nI%OB\9I>;p5Vs<_YkU;].K(chZJ,k8X96t ]!d?;H/|Jc:Hr-hhbBow![@FkT0xNOVXK|TO%Jg@Xz Date: Fri, 23 Jan 98 08:53:37 +0100 To: root Subject: Re: RANToid:RFC: pdb ; perl ; cgi-bin ; a MD box initial state build question Cc: chemistry@www.ccl.net Reply-To: Helmut.Heller@lrz-muenchen.de X-Reply-Format: NeXT Mail preferred X-Url: http://www.lrz.de/~heller --NeXT-Mail-801923790-14 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I got a message that there was an error and my posting could not be = transmitted, so I am trying again! Helmut Dear Eugene , You wrote: > The only thing short of absolute bliss would be a salt script, which > mutates a provided number of waters into, say, Na+Cl- pairs. Easy in = perl, > again. While you are downloading EGO, also get a friend of it, namely Solvate = from Helmut Grubm=FCller: [An attachment was originally included = here]http://www.mpibpc.gwdg.de/abteilungen/071/solvate.html It is much more advanced than my simple FORTRAN program AND it can place = ions around your protein/lipid of interest. And, after all, it works = nicely together with EGO [An attachment was originally included = here]:-)[An attachment was originally included here] > Next step to be taken, is building a lipid bilayer from above lego = blocks > (Helmut used Quanta, which afair is not free). I was thinking about > writing tlate-x , tlate-y , and mirror-z , With the EGO distribution comes a nifty utility, pdbpatch, which was = written by Marcus Eichinger, and which does just that! Call it without = parameters to get a basic usage summary. In interactiv mode type help for = more info. > (Btw, those of you who are eying DIY DSP-fueled MD > systems, should definitely check out Helmut Heller's (1993) Ph.D. work > (which, afaik, is unfortunately only available in German), as it = contains > yummy details about doing MD on a 60-node 4 MByte/node DIY Inmos > Transputer box). Thank you very much for this great recommendation[An attachment was = originally included here]:-)[An attachment was originally included here] = While what you say about the German part is undoubtedly true, we = published, out of Helmut Grubm=FCller's and my thesis, a paper in = Molecular Simulation which is in English and should be a bit more = accessible: @ARTICLEHELL90, author=3DHelmut Heller and Helmut Grubm"uller and Klaus Schulten, title=3DMolecular Dynamics Simulation on a Parallel Computer, journal=3DMS, volume=3D5, year=3D1990, pages=3D133--165, reference=3DPub.#~111 > Unfortunately, these are neutral > lipids, while my work is supposed to be about polycation-induced (btw, > polyelectrolyte MD also many CCL search hits do not make) lateral > segregation. What to do? Well, my first idea was just cut off that pesky > choline tail of some lipids (for chaperoning sake, interdigitating them > with neutral ones), and compensate one of the negative charges with, = say, > Na+. I think this can be done with X-PLOR (which is, imho, quite an > intimidating package), RasMol, or a one-time (perl) script. What is your > personal preference? I prefer to do such things with X-PLOR and I have some scripts (e.g., = POPC2DPPC.inp) which I could put on my WWW pages (which, btw., have moved = (and so have I [An attachment was originally included here];-)[An = attachment was originally included here] to a new location: [An attachment = was originally included here]http://www.lrz.de/~heller, new email: = heller@lrz.de) if there is some interest in them. Just let me know. I hope this helps a bit, later, Helmut P.S.: [An attachment was originally included = here]http://liposome.genebee.msu.su/cgi-bin/test did not work for me [An = attachment was originally included here]:-([An attachment was originally = included here] --- Servus, Helmut (DH0MAD) ______________NeXT-mail = welcome_________________ FAX: +49-89-280-9460 " Knowledge must be gathered and cannot be = given " heller@lrz.de ZEN, one of BLAKES7 Phone: +49-89-289-28823 = ----------------------------------------------------------------------------= ------- Dr. Helmut Heller =20 Leibniz-Rechenzentrum (LRZ) =20 High Performance Computing Group Barer Str. 21, Zi S2515, 80333 Munich, GERMANY =20 --NeXT-Mail-801923790-14 Content-Type: text/enriched; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I got a message that there was an error and my posting could not be = transmitted, so I am trying again! Helmut Dear Eugene , You wrote: > The only thing short of absolute bliss would be a salt script, which > mutates a provided number of waters into, say, Na+Cl- pairs. Easy in = perl, > again. While you are downloading EGO, also get a friend of it, namely Solvate = from Helmut Grubm=FCller: Next step to be taken, is building a lipid bilayer from above lego = blocks > (Helmut used Quanta, which afair is not free). I was thinking about > writing tlate-x <, tlate-y <, and mirror-z <, With the EGO distribution comes a nifty utility, pdbpatch, which was = written by Marcus Eichinger, and which does just that! Call it without = parameters to get a basic usage summary. In interactiv mode type help for = more info. > (Btw, those of you who are eying DIY DSP-fueled MD > systems, should definitely check out Helmut Heller's (1993) Ph.D. work > (which, afaik, is unfortunately only available in German), as it = contains > yummy details about doing MD on a 60-node 4 MByte/node DIY Inmos > Transputer box). Thank you very much for this great recommendation <:-) < While what you say about the German part is undoubtedly true, we = published, out of Helmut Grubm=FCller's and my thesis, a paper in=20 Molecular Simulation which is in English and should be a bit more accessible: @ARTICLEHELL90, author=3DHelmut Heller and Helmut Grubm"uller and Klaus Schulten, title=3DMolecular Dynamics Simulation on a Parallel Computer, journal=3DMS, volume=3D5, year=3D1990, pages=3D133--165, reference=3DPub.#~111 > Unfortunately, these are neutral > lipids, while my work is supposed to be about polycation-induced (btw, > polyelectrolyte MD also many CCL search hits do not make) lateral > segregation. What to do? Well, my first idea was just cut off that pesky > choline tail of some lipids (for chaperoning sake, interdigitating them > with neutral ones), and compensate one of the negative charges with, = say, > Na+. I think this can be done with X-PLOR (which is, imho, quite an > intimidating package), RasMol, or a one-time (perl) script. What is your > personal preference? I prefer to do such things with X-PLOR and I have some scripts (e.g., = POPC2DPPC.inp) which I could put on my WWW pages (which, btw., have moved = (and so have I=20 <;-) < to a new location:=20