CHARMM Development Project
Posted By: Ultros64 *** Topology file for AMP? *** - 03/06/07 07:58 PM
I'm trying to find CHARMM topology (and parameter?) file that defines AMP. The one I have, called top_all27_prot_lipid_na.inp, includes ADP and ATP but not AMP. I tried defining AMP in an analogous fashion to those two residue types, but the details are tricky to get exactly right. The file I've attempted to edit to include AMP is attached for those interested.

Anyone have any insight and/or a file I could use? Thanks!

Attached File
Posted By: lennart Re: *** Topology file for AMP? *** - 03/06/07 08:44 PM
AMP is a standard "oligonucleotide" consisting of one nucleotide. Have you tried something like (this for 5'AMP):

read sequence ade 1
gene amp first 5pho
Posted By: Ultros64 Re: *** Topology file for AMP? *** - 03/06/07 09:29 PM
That's a good idea to consider AMP just a "short oligonucleotide" of type ADE, though my molecule still has a few extra atoms compared to the definition of ADE in the topology file. Also, I'm not familiar with the syntax of the two lines you used above -- could you elaborate please?
Posted By: lennart Re: *** Topology file for AMP? *** - 03/06/07 09:39 PM
Then it is perhaps not 5'AMP you have? 3'AMP is generated with appropriate FIRST and LAST patches specified to the GENErate command (5TER, 3PHO); see the topology (RTF).
Still I suppose you could start from 5'AMP/3'AMP and add your extra atoms. Note that you probalby also need to patch it, after the GENErate, to be a deoxyribose and that the generate command may need a "LAST 3TER".

The commands are standard CHARMM commands for generating a "PSF". See examples in the Script Archive forum, the CHARMM doucmentation and the CHARMM Course forum as well as tutorials available under LINKS on www.charmm.org.
Posted By: Ultros64 Re: *** Topology file for AMP? *** - 03/09/07 07:55 PM
Thanks for the advice; I'll give one of those things a try.

However, it is suprising to me that apparently so few NAMD users have a topology file containing a molecule as biologically relevant as AMP. If anyone has such a file I would, of course, be grateful to get a hold of it.
Posted By: rmv Re: *** Topology file for AMP? *** - 03/09/07 08:18 PM
As already noted, it should be straightforward to create what you want within the context of CHARMM, probably even for cAMP. Since this is a CHARMM site, you'd have to look elsewhere to find what NAMD users have available (like maybe a NAMD support site).
Posted By: lennart Re: *** Topology file for AMP? *** - 03/09/07 09:11 PM
I don't think there is such a thing as a "NAMD topology for AMP" since NAMD is a program without a force field of its own. This should however not be a problem since all DNA force fields (including the CHARMM force field) contain AMP.
Posted By: Ultros64 Re: *** Topology file for AMP? *** - 03/09/07 09:25 PM
Of course, you are right that 'there is such a thing as a "NAMD topology for AMP."' I meant to say a CHARMM topology file for AMP.

Unfortunately, the CHARMM topology files I have (and I have looked through each of them extensively) do not explicitly define a residue type called "AMP", so I'm trying to decide what the best course of action is for "inventing" such a definition to adequately describe adenosine monophosphate. So that's my problem at hand.

As for the previous poster, that's a good idea to check out what some forums specifically oriented toward NAMD have to offer in this regard. It's sure worth a try!
Posted By: rmv Re: *** Topology file for AMP? *** - 03/09/07 09:50 PM
The CHARMM FF often uses a patch (PRES) for simple changes that make new molecules, such as protonating Asp, or adding 3' or 5' PO4 to a chain of one or more nucleotides. What this means is that separate residues for small changes are not needed, and simple CHARMM commands (as given above by Lennart) can be used to make the change. Surely NAMD must have a patching mechanism, if it fully supports the CHARMM FF ...
Posted By: lennart Re: *** Topology file for AMP? *** - 03/09/07 09:59 PM
It is not unfortunate that the CHARMM RTF does not define AMP since that would be a duplication of something that already exists.
The residue you want is named ADE (for adenine) - AMP means Adenine MonoPhosphate - and then you apply the appropriate patches to get the 5' and 3' terminations (5┬┤phosphate and 3' hydroxyl) that you want; note that you will probably also need to apply a patch to make the sugar a deoxyribose. All this is very, very easy to do in CHARMM.
Posted By: Ultros64 Re: *** Topology file for AMP? *** - 03/09/07 10:13 PM
Now I understand that altering ADE by the patch method is the way to go. Thank you for explaining this thoroughly.

That leads me to my next question: What is the syntax for embedding these patch commands into a tcl script readable by VMD instead of as CHARMM command input?

Here's the reason I ask this. I know this is a CHARMM forum that's not specifically dedicated to other software that uses CHARMM parameters, such as VMD, but from what I can tell from charm.org, the makers of CHARMM charge a $600 licensing fee for their command line-driven program. If there's another way to generate the relatively small quantity of code I apparently need to accomplish this patch, that would of course be optimal.

I'll keep trying variations on the earlier poster's GENE and PATC phrases with "3ter" and "5pho," but haven't had any luck so far, so if anyone knows the proper few lines of text to append to the ADE topology entry, that would be great.

You've been very helpful so far. Thanks in advance...
Posted By: rmv Re: *** Topology file for AMP? *** - 03/09/07 10:58 PM
GENER and PATCH are specific CHARMM commands, and are not used or recognized in the topology file; you must determine the equivalent NAMD commands (psfgen?) and how to use them.

The $600 fee is a terrific bargain, compared to the cost of buying CHARMm from Accelrys; because of the commercial variant, the academic version cannot be freely distributed.
Posted By: Dan_B Re: *** Topology file for AMP? *** - 03/11/07 03:43 AM
Instead of using a TCL script, you could just make your PSF in charmm, and convert it to a NAMD format PSF using a utility on the NAMD website, I think it's called charmm2namd. You can do the same thing with a coordinate file (crd2pdb).

I'd recommend doing all your model building and analysis in CHARMM, it's much much easier than anything with tcl scripts.. part of the reason the 600$ is well worth it.
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