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Setup, I/O, and Basic questions Jump to new posts
Re: Mistakes when building crystal Allen_123 05/28/20 08:57 AM
I think there might be another bug in translation of unit cell(Noper=0) for hexagonal type crystal. I got pdb of unit cell of same P61 crystal from CCDC and implemented into Charmm, and run a short NPT simulation after minimization. There was no error, but the IMNBvdw term was extremely large (28826012849). I wrote the image atoms and found an overlap of two unit cells([img][/img]) The correct packing should look like this [img][/img]
8 2,745 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: EOF during read rmv 05/27/20 03:41 PM
Check the log from the previous run for errors; there are some cases where an error generates a bad restart file.

Try reading the coordinates, delta coordinates, and velocities via READ COOR DYNR as a test.
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Minimization, Normal modes, Monte Carlo,... Jump to new posts
Re: hydrogen-only minimization hedderic 05/21/20 05:09 PM
Thats true, but exactly thats why I introduced the new patches, in order to delete the introduced bonds and energy terms between non-connected residues and build new connections to the caps (the coordinates of the caps are already present in the pdb).

bomlev was just for test purposes, ommitting it led to no further warnings or would terminate the calculation.

Furthermore, hydrogens that do not belong to any patches residue or that are near breaks are sometimes also minimized in a weird way, so I am guessing that the problem more or less is the starting structure and minimization strategy.
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Molecular Dynamics Jump to new posts
Re: incorrect density when using VV2 to run drude rmv 05/19/20 02:39 PM
For parallelpiped unit cells, i.e. those with six parallel faces, the minimum number is 26, which is one image per face, edge, or vertex. The unit cell is at the center of a 3x3x3 array, completely surrounded by 26 image cells. (Crystal unit cells with edges shorter than the nonbond cutoff require additional images to satisfy the nonbond list building.) The exceptions to 26 are typically the more spherical shapes, such as the rhombic dodecadedron and the truncated octahedron, which require fewer images to completely surround the unit cell, e.g. 12 for the dodecahedron.
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Installation and Testing Jump to new posts
Re: Simulation error in MPI parallel but not in one processor lennart 05/14/20 09:24 AM
In lactose there are lone-pairs (Drudes) on atoms in the linkage between the two residues. These atoms then are from different groups, and this is not handled well in parallel, probably because the atoms may be on different processors.
I would suggest that you try making a single RESI LACT in the rtf, and make sure that all atoms required in the defintion of a lone-pair are in the same group, as defined by the GROUP statments in the RTF. DO NOT MAKE THE WHOLE RESIDUE INTO A SINGLE GROUP. Groups should be no larger than 12Å across.
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Setup, I/O, and Basic questions Jump to new posts
Re: Issue of goto command in loop lennart 05/13/20 10:38 AM
You cannot use input redirect ("<") with MPI and CHARMM goto statements. The correct way to run charmm is to use the "-i" flag instead:
(mpirun -np 2) charmm -i input_file.inp
1 59 Read More
CHARMM-GUI Jump to new posts
Re: Using Drude Prepper to generate a solvated protein Michael Robinson 05/12/20 08:28 AM
A follow up that's related to the original question - I've been doing some testing with CharmGUI's Drude Prepper once more, and I've realised that the error described in the original post only occurs for peptides with a disulfide linkage present. Drude Prepper is explicitly listed as handling disulfide linkages, and so I hadn't thought to test this. My example, to aid in replication of this behaviour and explain the method used, involves using Solution Builder to create a solvated system from the 3i3z PDB crystal structure. The results from this solvation are then used as input for Drude Prepper, but a fatal error occurs in Stage 2 of the Drude Prepper module if any of the 3 disulfide linkages present in the 3i3z crystal structure were added using the Solution Builder module. I'm aware of Rick's previous comments related to handling this with CHARMM/charmm, but as this is something that CHARMM-GUI is stated to handle, I thought it was worth asking: is this a known issue, user error, or something else? Thanks for any help with this matter!
3 357 Read More
Installation and Testing Jump to new posts
Re: Multiple times printed output while using MPI rmv 05/11/20 04:15 PM
What is most important is the mpi.mod file, which provides the Fortran90 interface for the MPI implementation; in my experience, the build has failed when mpi.mod was created with a different gfortran version than the one being used to compile CHARMM.
7 230 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Generate PSF for already protonated / patched PDB file rmv 05/10/20 06:31 PM
Note that for output logs, coordinate files, long input scripts, etc., we highly recommend attaching them as files with a .txt extension, as web browsers can easily display them in a fixed font, and they can be easily viewed in a separate tab or window. It's much easier to read everything that way. Please review READ BEFORE POSTING.

The missing improper terms are listed for the first and last residues, not the first two. This is expected, as the definitions in the RTF refer to atoms in previous or next residues, and those do not exist for the N-term and C-term residues; it is an expected end effect.

The PDB file is probably missing either an END statement or a blank line following the last ATOM record.
4 159 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
is this possible in resd? jamesmao 05/07/20 07:45 AM
I use resd to restrain distance between two atoms (R) not go beyond a certain value (A1) and it works well. For some unknown reason, the MD (using openmm) ignores the image command from charmm. As a result, sometimes the simulation stops due to R jumps to a huge number. I am wondering if it is possible to set up restraint this way: include the restraint only when A1
My current resd is:
resd kval 10.0 rval 9.06 positive ival 1 -
     1.0 DNAA 17 N2  DNAA 16 O2 -
     1.0 DNAA 17 N1  DNAA 16 N3 -
     1.0 DNAA 17 O6  DNAA 16 N4

So the restraint works when R>9.06. Is it possible to make it working for 10>R>9.06?

Thank you.
0 56 Read More
CHARMM-GUI Jump to new posts
Rattle Algorimth error Asma 05/07/20 07:12 AM
Dear users,

I have run six steps of equilibration from the input files that CHARMMGUI generated. As soon as I start production run I get " constraint failure in Rattle algorithm for atom xxxx". after some research I believe that a potential solution is to heat the system slowly but I have already equilibrated the system now using 303.15 for all equilibration steps, so I wonder if slow heating now can would helpt? or is there another solution I can do so that my system overcome this problem.?

Thank you
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Parameter Set Discussion Jump to new posts
Re: Rattle Error - unstable system at end of equilibration rmv 05/06/20 02:49 PM
This does not seem to be a question about force field parameters. Note that there is a specific forum here for CHARMM-GUI questions, and this isn't it.
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Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Re: Selection in Energy Calculation ca4930 05/04/20 09:28 PM
Thanks - I should've thought of that!
2 75 Read More
Parameter Set Discussion Jump to new posts
Re: CHARMM parameters for Mn2+ rmv 05/03/20 04:44 PM
As you may have noticed, the answer to this question has not changed for the past 16 years or more.

How you approach this depends on the importance of the Mn++ binding site in the study being considered. If you only need it as a structural element, unrelated to the rest of the study, stabilizing the preferred binding geometry with restraints may be the best approach. For that, you should undertake a review of relevant crystal structures, esp. those with good resolution for the complexation site, to determine a reasonable geometry.
1 84 Read More
Parameter Set Discussion Jump to new posts
Re: Cholesteryl oleate parameters rmv 05/01/20 12:34 AM
The preferred approach is to use CGenFF on a small fragment that represents the linkage, and then define a new residue where only the linkage uses any of the newly derived parameters, with the existing FF used as much as possible. The QM may be needed if the penalties are large, but may not be needed for this case.
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