Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
Joined: Mar 2007
Posts: 5
U
Forum Member
OP Offline
Forum Member
U
Joined: Mar 2007
Posts: 5
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 Images
Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
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


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Mar 2007
Posts: 5
U
Forum Member
OP Offline
Forum Member
U
Joined: Mar 2007
Posts: 5
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?

Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Mar 2007
Posts: 5
U
Forum Member
OP Offline
Forum Member
U
Joined: Mar 2007
Posts: 5
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.

Joined: Sep 2003
Posts: 8,621
Likes: 24
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,621
Likes: 24
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).

Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Joined: Mar 2007
Posts: 5
U
Forum Member
OP Offline
Forum Member
U
Joined: Mar 2007
Posts: 5
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!

Joined: Sep 2003
Posts: 8,621
Likes: 24
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,621
Likes: 24
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 ...

Joined: Sep 2003
Posts: 4,861
Likes: 10
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,861
Likes: 10
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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Page 1 of 2 1 2

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.5
(Release build 20201027)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.010s Queries: 36 (0.005s) Memory: 0.7820 MB (Peak: 0.8913 MB) Data Comp: Off Server Time: 2022-11-29 15:10:36 UTC
Valid HTML 5 and Valid CSS