VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Apr 17 2014 - 10:27:43 CDT

Hi Norge,

Ahh. Ok. That makes sense. :) I can't think of a VMD-based solution
other than to generate a psf directly from the molecule.pdb (using
psfgen) and then do the merger. This might be messy, since the atomnames
Amber and Charmm assume may not overlap completely, but if the pdb
atomnames are what Charmm expects, it is probably your easiest way
forward that involves VMD. It will still be hard. Carbohydrates and
glycopeptides in CHARMM can be messy due to the linkages required for
proper simulation (and since you are using glycam, I assume that's what
you are interested in). The process is certainly doable (see the added
lines below detailing how to use psfgen to build the patches between
sugar residues), but it may actually be simpler to convert your
subsystem to Amber format (Using CHAMBER) and do the combination in
Amberland, but I am not familiar with the tools the Amber community has
to do that sort of thing.

-Josh Vermaas

If you want to deal with carbohydrates and glycopeptides in CHARMM, here
is a section of a script to build a carbohydrate section, taken from a
script I made to build up the carbohydrate chains present in some
antibody crystal structures:

#Load the appropriate topology files. I had to split apart the
glycopeptide section into the topology only portion, as psfgen can't
handle the original stream file
topology toppar/top_all36_carb.rtf
topology toppar/top_all36_prot.rtf
topology toppar/stream/top_all36_carb_glycopeptide.inp

#Lots of boring protein-related stuff would be here...

#Now build up the sugar parts, which in this case needed to be linked to
the protein.
segment SB {
    first none
    last none
    pdb sugarB.pdb
}
coordpdb sugarB.pdb SB
#Protein-sugar patch
patch NGLB PB:314 SB:475
#Mess of carbohydrate patches
patch 16bb SB:475 SB:476
patch 14bb SB:475 SB:477
patch 14bb SB:477 SB:478
patch 16ab SB:478 SB:479
patch 12ba SB:479 SB:480
patch 14bb SB:480 SB:481
patch 13ab SB:478 SB:482
patch 12ba SB:482 SB:483

#Normal guess commands here

On 04/17/2014 10:08 AM, Norge Cruz Hernández wrote:
>
> Hi Josh,
>
> I can perform molecular dynamics simulations by using the files
> molecule.top and molecule.crd. i.e., input in AMBER file format. So, I
> can perform it by using " amber on", "parmfile molecule.top" and
> "ambercoor 4_gg.crd". It worked.
>
> However, I need to perform molecular dynamics simulations in a system
> "A+molecule", but the input files for subsystem A are A.pdb and A.psf,
> i.e., file format to be used by NAMD. So, I was thinking the way to
> convert molecule.top and molecule.crd >=to=> molecule.psf and
> molecule.pdb, and put it all together by using "Merge Structures" in
> vmd. I know, that it is possible to get the molecule.pdb file from
> molecule.crd and molecule.top. However, I was not able to get the .psf
> file comming from this pdb file.
>
> That is the point ... can you help me ...
>
> Thanks !!!
>
> ---
> Prof. Norge Cruz Hernández
> Dpto. Física Aplicada I
> Escuela Técnica Superior de
> Ingeniería Informática
> Universidad de Sevilla
> ave: Reina Mercedes, 41012
> Sevilla, Spain
> Phone number: +34 - 954559970
> Fax number: +34 - 954554341
> http://www.personal.us.es/norge/
>
> El 16/04/2014 21:29, Josh Vermaas escribió:
>
>> Hi Norge,
>>
>> Because of how the forcefields are laid out, I don't think there is a
>> straightforward tool to convert from Amber to Charmm formats. CHAMBER
>> exists to do the reverse process (dx.doi.org/10.1002/qua.22372), but
>> I don't think there is much of a market in converting the other way
>> around, mostly because of how the files are laid out. NAMD cares
>> about atom-type names when looking up parameters to run simulations,
>> names that do not directly correspond to those used in Amber. CHARMM
>> is worse, since it looks up parameters based on atom-type numbers,
>> which definitely don't correspond to those in Amber. So any such
>> script would have to writeout the parameters contained in the parmtop
>> file in a CHARMM-format parameter set. Such a set of parameters
>> wouldn't be applicable to anything but that exact simulation system
>> (since it would be missing lots of terms needed in general), leading
>> to a flood of tiny parameter files to keep track of.
>>
>> To avoid the need for this, NAMD can use Amber formatted files
>> directly for input purposes
>> (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html), and VMD
>> can load them just fine for visualization and analysis purposes (the
>> Amber community has a number of minitutorials around, such as at
>> http://ambermd.org/tutorials/basic/tutorial2/). You could load the
>> molecule.top and molecule.crd into VMD and write out a fake psf from
>> there, but it would in no way be suitable to run a simulation and I
>> really wouldn't recommend it.
>>
>> -Josh Vermaas
>>
>> On 04/16/2014 01:24 PM, Norge Cruz Hernández wrote:
>>>
>>> Hi,
>>>
>>> I am new performing molecular dynamics simulations by using NAMD. I
>>> have obtained the AMBER format files (molecule.top, molecule.pdb and
>>> molecule.crd) by using link:
>>> http://glycam.ccrc.uga.edu/ccrc/carbohydrates/cb_newbuilder.jsp?tool=crystallography&option=ff99:glycam06.
>>> However, I would like to convert such files to the CHARMM format
>>> file .psf and .crd or NAMD format file .psf and pdb. Please, could
>>> you like to recommend me any software ... or script.. to convert
>>> (molecule.top and molecule.crd) in AMBER format =to=> (molecule.psf
>>> and molecule.crd) in CHARMM format or (molecule.psf and
>>> molecule.pdb) in NAMD format?
>>>
>>>
>>>
>>> Thanks in advance !!!
>>>
>>> --
>>> Prof. Norge Cruz Hernández
>>> Dpto. Física Aplicada I
>>> Escuela Técnica Superior de
>>> Ingeniería Informática
>>> Universidad de Sevilla
>>> ave: Reina Mercedes, 41012
>>> Sevilla, Spain
>>> Phone number: +34 - 954559970
>>> Fax number: +34 - 954554341
>>> http://www.personal.us.es/norge/