[gmx-developers] Fwd: Re: using replace/delete syntax of termini database for specbond

Pär Bjelkmar bjelkmar at cbr.su.se
Wed Aug 25 16:18:51 CEST 2010

Sorry for the subject in my last post.

Vidarebefordrat brev:

> Från: Pär Bjelkmar <bjelkmar at cbr.su.se>
> Datum: 25 augusti 2010 14.32.23 CEST
> Till: gmx-developers at gromacs.org
> Ämne: Re: gmx-developers Digest, Vol 76, Issue 15
> Hi,
> It's something similar to what CHARMM does. They use a lot of such special linkages to combine existing "residues" into new ones, all protonation states for example but also some much more complicated things like "building" the DPPC lipid from Palmitate (PALM) and "PCGL", using two linkages (EST1 and EST2), called patches in CHARMM. 
> And this is also, I guess(?), why you, Roland, used the trick with the modified psfgen program (NAMD/VMD software) to build GROMACS topologies of your lignin and cellulose molecules: it could build the molecules modularly using the patches.
> Regarding the CHARMM port: this modularity is why it's kind-of hard to port the CHARMM ff "completely".
> /Pär Bjelkmar
>> Message: 1
>> Date: Tue, 24 Aug 2010 19:44:07 -0400
>> From: Roland Schulz <roland at utk.edu>
>> Subject: [gmx-developers] using replace/delete syntax of termini
>> 	database	for specbond
>> To: Discussion list for GROMACS development
>> 	<gmx-developers at gromacs.org>
>> Message-ID:
>> 	<AANLkTim5=wX060wcv29XxuApPXdhEK8DLYnxg9dn23a_ at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>> Hi,
>> it would be very nice if it would be possible to use the replace/delete/add
>> features of the termini (tdb) files also in combination with specbond. This
>> would make it simpler to specify some non-standard linkages.
>> As an example: Instead of fully specifying the CYS2 it would be nice to be
>> able to say:
>> [ CYS2 ]
>> [ replace ]
>>   CB    opls_214    12.011 0.0975
>>   SG    opls_203   32.06500 -0.2175
>> [ delete ]
>>   HG
>> For this example the saving would be very limited. But with a large number
>> of possible linkages this would give a considerable saving in specifying the
>> topology for possible combinations of linkages. The residue used as basis
>> (CYS) for the modified residue (CYS2) could come from the beginning of the
>> name or could be specified explicitly. This modified residue could be used
>> by a specbond line (which wouldn't change from the current line using
>> CYS2). It seems this feature  could be implemented by a very limited patch
>> because it would use only features already implemented for termini. But I
>> don't understand the termini code so I can't judge this myself. Also I'm not
>> sure whether it might be a problem with the charge groups.
>> Would this be something easy and useful to add to pdb2gmx?
>> Roland
>> -- 
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
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