[gmx-users] Unknown cmap torsion between atoms

[xiang_ning at yahoo.com]

Dear Justin,


Thanks a lot! I deleted the forcefield at the end of the top file and missed the forcefield at the beginning! Now I can run the minimization. Thanks again for all your assistance!

Best regards,

Ning





From: Xiang Ning
Sent: ‎Wednesday‎, ‎August‎ ‎27‎, ‎2014 ‎5‎:‎20‎ ‎PM
To: Justin Lemkul, gromacs.org_gmx-users at maillist.sys.kth.se






Dear Justin,




Thank you very much for your assistance. I divided the system into protein, lipid, water and ions, and ran pdb2gmx to obtain the top files, and converted the top files to itp files by deleted force filed file, [system] and [molecules] in the end of the top files. And then, I combine these files into one top file: system.top, it is like the below:




; Include forcefield parameters

#include "./charmm36.ff/forcefield.itp"




; Include protein topology

#include "pep.itp"




#ifdef POSRES

#include "posre.itp"

#endif




; Include lipid topology

#include "POP.itp"




; Include water topology

#include "./charmm36.ff/tip3p.itp"




#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

;  i funct       fcx        fcy        fcz

   1    1       1000       1000       1000

#endif




; Include topology for ions

#include "./charmm36.ff/ions.itp"




[ system ]

; Name

Protein




[ molecules ]

; Compound        #mols

Protein             1

Other2              1



SOL              1776




However, there is a fatal error when I used this system.top ran "grompp -f minim.mdp -c system.gro -p system.top -o system.tpr":

Syntax error - File forcefield.itp, line 9

Last line read:

'1      2       yes     1.0     1.0'

Found a second defaults directive.




I would like to know, how can I combine the itp files into one correct top file? 




Thank you very much!




Best regards,

Ning














On Wednesday, August 27, 2014 11:41 AM, Xiang Ning <xiang_ning at yahoo.com> wrote:
 







Dear Justin,




Sorry I missed the reply for yesterday. So the atoms are mostly from my peptide: 319: atom C of VAL, 321: N of ILE, 323: CA of ILE, 338, C of ILE, and one from lipid POPC: 341: atom N of POPC. I just used "pdb2gmx -f box.gro -p box.top" to obtain the top file of the whole system, which including water, protein, lipid and ions. It generated several itp file and one top file. The CMAP is in "box_Protein.itp", which included the itp file of protein and lipid. After that, I ran grompp, and then the problem "unknown cmap torsion" occurred. I think the torsion was because it can not tell apart the last peptide atom and the first lipid atom. Could you please let me know how to solve this problem? Thanks a lot!




Best,

Ning









On Wednesday, August 27, 2014 10:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
 






On 8/27/14, 10:14 AM, Xiang Ning wrote:
> Hi all,
>
> I was trying to put a protein inside the membrane (generated by Charmm-Gui and I made some modification). I used "editconf -f protein.gro -o conf.gro -box (my box demension x y z)" and then "genbox -cp conf.gro -cs lipid_water_ion.gro -o box.gro" to remove the overlapped lipids. It looks fine in VWD, no overlap between protein and lipids occurred, but when I ran "grompp -f minim.mdp -c box.gro -p box.top -o box.tpr", it showed "Unknown cmap torsion between atoms 319 321 323 338 341". I try to built the box in several other ways, this problem kept occurring. So I searched for previous solution, and found the patch "0001-Fix-pdb2gmx-merge-cmap.patch" may fix the problem. However, I cannot use this patch because it needs to install in the source directory, but the Gromacs 4.5 I used is installed in our university system, I am not able to put the patch in the source directory.
>
> So I would like to know, can I put the patch in my work directory to make it work? It asked "file to patch" if I put it in my work directory, so which file I need to patch? Or are there any other method can solve the problem for "Unknown cmap torsion between atoms"? I used charmm36 force field for all atom by the way.
>
> Thanks very much for your attention and assistance!

>

See reply from yesterday:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091771.html

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==================================================