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#1980 07/08/04 12:48 PM
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Hello

For a current project I need parameters for SAM (S-adenosyl methionine). I came across at least one publication where they run simulations on a SAM-containing enzyme, but unfortunately no parameters were given.
So if anybody here is aware of SAM parameters and willing to share them, I would greatly appreciate.
Otherwise I will have to try to stitch them together from parameters for Ado and Met.

Thanks to all respondents

Hans
---
Dr. Hans Martin Senn
Max Planck Institute for Coal Research
D-45470 Mülheim an der Ruhr, Germany


......................................................................... Dr Hans Martin Senn University of Glasgow Department of Chemistry Glasgow G12 8QQ, Scotland/UK
hmsenn #1981 07/17/04 09:26 PM
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We've put together SAH parameters, but not SAM. Let me know if you need
them. Note that SAM will take a little work as the charged nature around the
sulfur has not been treated previously.

alex



School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
alex #27860 07/06/11 12:44 PM
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Could you send me the SAH parameters to my email adress wanxiaobo@nibs.ac.cn , I would how to add the reasonable charges of SAM based on the SAH.

alex #30014 05/19/12 09:40 AM
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Hi,

I am working on a protein that needs S-adenosyl methionine as a co-factor. I intend to do some MD on the protein.
I came across this post and was wondering if these parameters could be shared with me ?

Thanks in advance,
Manali

manali #30024 05/21/12 07:13 AM
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Hi,

In line with my previous email (getting S-adenosyl methionine params) i tried to submit a mol2 file of S-adenosyl methionine generated by Discovery studio to ParamChem.
I got the following error:

attype warning: unknown sulfur type not supported;
skipped molecule.

Does this mean ParamChem will not work for S-adenosyl methionine ?
What is a work around? I have no experience with generation of parameters.

Any help will be greatly appreciated.

Thanks
Manali

hmsenn #30025 05/21/12 07:55 AM
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There is a patch (PRES SAM in toppar/stream/toppar_prot_na_all.str) to create SAM from ADE.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
lennart #30082 06/07/12 08:24 AM
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Dear Lennart,

Thanks for your suggestion.
The protein i am working on has a co-crystallised S-adenosyl methionine.

When i used the Patch command "patch SAM SADM 1 SETUP WARN"
(where SADM is the segid) with my entire ligand from PDB as input i got a structure of SAM with no bond between Sulfur and CG, moerover the geometry of the amino acid part was distorted.(see img: SAM_broken)


Then i edited the crystal SAM such that it only had adenosine.
On applying patch command as above the SAM structure was getting generated properly, but the placement of methionine coordinates were obviously not matching the crystal.

Then i tried to patch the parameters of adenine and the patch SAM together to define a residue called SAM in the topology file. For some reason i am not able to get any bonds between the CGP and HGP1,2,3(see img SAM_Hproblem)

I have attached the SAM parameters in a separate file (that i included as part of top_all27_prot_na_mod.rtf)
I have checked that there are bond definitions for the concerned atoms as well as IC entries.
However in the output i get the error:

: No angle parameters for 33 ( CT2 CT2 SP )
: No angle parameters for 35 ( HA CT2 SP )
: No angle parameters for 36 ( HA CT2 SP )
: No angle parameters for 37 ( CT2 SP CN8B)
: No angle parameters for 38 ( CT2 SP CT3 )
: No angle parameters for 39 ( CN8B SP CT3 )
: No angle parameters for 40 ( SP CN8B HN8 )
: No angle parameters for 41 ( SP CN8B HN8 )
: No angle parameters for 42 ( SP CN8B CN7 )
: No angle parameters for 46 ( SP CT3 HA )
: No angle parameters for 47 ( SP CT3 HA )
: No angle parameters for 48 ( SP CT3 HA )


I am not able to figure out what these are.


The following is the input file :


OPEN UNIT 10 CARD READ NAME top_all27_prot_na_mod.rtf
READ RTF CARD UNIT 10
CLOSE UNIT 10

OPEN UNIT 12 CARD READ NAME par_all27_prot_na.prm
READ PARA CARD UNIT 12
CLOSE UNIT 12


open read unit 60 card name "SAM2.pdb"
read sequ pdb unit 60
generate SADM SETUP
REWIND UNIT 60
READ COOR PDB UNIT 60
CLOSE UNIT 60

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD

open unit 1 write card name SAM_new2.psf
write psf card unit 1

open unit 1 write card name SAM_new2.pdb
write coor pdb unit 1


STOP

Please let me know if what i have done is reasonable & where i am going wrong.
Help is very greatly appreciated.

-Manali

Attached Images
SAM_broken.jpg SAM_Hproblem.jpg
SAM_final_params.txt (9.5 KB, 735 downloads)
hmsenn #30085 06/07/12 01:55 PM
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If the patch works for adenine/SAM alone, it should work for your entire system. You should read the Met coordinates from the PDB, not have them generated by CHARMM. Is SAM the first residue in your SADM segment?

The lack of lines between the carbon and hydrogens may be s simple visualization artifact.

The error messages about missing parameters refer to the chemical type (not the IUPAB) names of the atoms. These parameters have to be in a parameter file that you read into CHARMM.

Your file SAM_final_params.txt does not contain any parameters, it is just the RTF.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
lennart #30091 06/08/12 06:50 AM
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Dear Lennart,

For some reason its working now!

I am able to read in the entire crystal S-adenosyl methionine coords as ADE and apply the PATCH SAM.

There are no broken /improper bonds as before.


Thanks
Manali

hmsenn #30563 08/25/12 10:07 AM
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Hi,

I am still having problems with SAM.
I build it in as follows:


OPEN UNIT 10 CARD READ NAME top_all27_prot_na.rtf
READ RTF CARD UNIT 10
CLOSE UNIT 10

OPEN UNIT 12 CARD READ NAME par_all27_prot_na.prm
READ PARA CARD UNIT 12
CLOSE UNIT 12


open read unit 60 card name "dnmt.pdb"
read sequ pdb unit 60
generate DNMT SETUP
REWIND UNIT 60
READ COOR PDB UNIT 60
CLOSE UNIT 60

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD


open read unit 12 card name "zinc.pdb"
read sequ pdb unit 12
generate ZINC SETUP
REWIND UNIT 12
READ COOR PDB UNIT 12
CLOSE UNIT 12

stream toppar_prot_na_all.str

open read unit 61 card name "SAM_orig.pdb"
read sequ pdb unit 61
generate SADM SETUP
patch SAM SADM 1261 SETUP WARN
REWIND UNIT 61
READ COOR PDB UNIT 61
CLOSE UNIT 61

IC FILL PRESERVE
IC PARAMETERS
IC BUILD
HBUILD


Write out psf, pdb, crd files


When i try to do an energy minimization on the system using the psf and crd, SAM breaks up as shown in the picture.

When a patch command is used to build SAM, shouldnt all SAM parameters be written to the psf file?

Am i missing something ? What is going wrong here ?

Thanks in advance,

Manali

Attached Images
brokenSAM.jpg
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