VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Wed Jul 05 2023 - 02:53:00 CDT

Hi,

I wrote out the backbone dcd file for each trajectory using the following commands:

catdcd -o MD_backbone_Neg_Control_1.dcd -otype dcd -i indexfile -dcd MD_protein_Neg_Control_1.dcd

catdcd -o MD_backbone_Neg_Control_2.dcd -otype dcd -i indexfile -dcd MD_protein_Neg_Control_2.dcd

catdcd -o MD_backbone_Neg_Control_3.dcd -otype dcd -i indexfile -dcd MD_protein_Neg_Control_3.dcd

etc.

Then, I used catdcd again to combine all of the backbone trajectories with this command:

catdcd -o all_combined.dcd -i indexfile MD_protein_Wildtype_1.dcd MD_protein_Wildtype_2.dcd MD_protein_Wildtype_3.dcd MD_protein_Neg_Control_1.dcd MD_protein_Neg_Control_2.dcd MD_protein_Neg_Control_3.dcd ....

This combined all the files, but there seems to be an issue with the combined trajectory. When I run PCA analysis with Bio3d on the merged trajectory, and look at the contribution of each residue to PC1, I see that there are several residues which appear to be missing. I loaded the DCD into VMD and it has the correct number of atoms I expect from the index file, but it does not look like the original protein chains I was simulating (it looks mushed together).

Checking the output file of the catdcd combining I ran on a supercomputer, I see the following:

------------------------------------------------------------------
Info) Dynamically loaded 2 plugins in directory:
Info) /shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/molfile
*** Error in `/shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/bin/catdcd5.1/catdcd': double free or corruption (!prev): 0x00000000010d1140 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2af553da0329]
/shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/bin/catdcd5.1/catdcd(atan+0x1b93)[0x40a743]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2af553d41555]
/shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/bin/catdcd5.1/catdcd(fmod+0x8a)[0x408e9a]
======= Memory map: ========
00400000-005ab000 r-xp 00000000 67:70864 144115274109512152 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/bin/catdcd5.1/catdcd
006aa000-006bd000 rw-p 001aa000 67:70864 144115274109512152 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/plugins/LINUXAMD64/bin/catdcd5.1/catdcd
006bd000-006c7000 rw-p 00000000 00:00 0
010c3000-01100000 rw-p 00000000 00:00 0 [heap]
3f8a200000-3f8a220000 r-xp 00000000 67:70864 144115274109512127 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/libexpat.so.0
3f8a220000-3f8a320000 ---p 00020000 67:70864 144115274109512127 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/libexpat.so.0
3f8a320000-3f8a322000 rw-p 00020000 67:70864 144115274109512127
/shared/ucl/apps/vmd/1.9.3/text-only/lib/libexpat.so.0
2af5530d4000-2af5530f6000 r-xp 00000000 08:03 148055 /usr/lib64/ld-2.17.so
2af5530f6000-2af5530fb000 rw-p 00000000 00:00 0
2af55310e000-2af55310f000 rw-p 00000000 00:00 0
2af55310f000-2af55319b000 r-xp 00000000 67:70864 144115274109512138 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/libsqlite3.so.0
2af55319b000-2af55329a000 ---p 0008c000 67:70864 144115274109512138 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/libsqlite3.so.0
2af55329a000-2af55329e000 rw-p 0008b000 67:70864 144115274109512138 /lustre/shared/ucl/apps/vmd/1.9.3/text-only/lib/libsqlite3.so.0
2af55329e000-2af5532a4000 rw-p 00000000 00:00 0
2af5532f5000-2af5532f6000 r--p 00021000 08:03 148055 /usr/lib64/ld-2.17.so
2af5532f6000-2af5532f7000 rw-p 00022000 08:03 148055 /usr/lib64/ld-2.17.so
2af5532f7000-2af5532f8000 rw-p 00000000 00:00 0
2af5532f8000-2af5532fa000 r-xp 00000000 08:03 148247 /usr/lib64/libdl-2.17.so
2af5532fa000-2af5534fa000 ---p 00002000 08:03 148247 /usr/lib64/libdl-2.17.so
2af5534fa000-2af5534fb000 r--p 00002000 08:03 148247 /usr/lib64/libdl-2.17.so
 2af5534fb000-2af5534fc000 rw-p 00003000 08:03 148247 /usr/lib64/libdl-2.17.so
2af5534fc000-2af5535e7000 r-xp 00000000 67:70864 144115273706872383 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libstdc++.so.6.0.20
2af5535e7000-2af5537e7000 ---p 000eb000 67:70864 144115273706872383 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libstdc++.so.6.0.20
2af5537e7000-2af5537ef000 r--p 000eb000 67:70864 144115273706872383 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libstdc++.so.6.0.20
2af5537ef000-2af5537f1000 rw-p 000f3000 67:70864 144115273706872383 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libstdc++.so.6.0.20
2af5537f1000-2af553806000 rw-p 00000000 00:00 0
2af553806000-2af553907000 r-xp 00000000 08:03 148444 /usr/lib64/libm-2.17.so
2af553907000-2af553b06000 ---p 00101000 08:03 148444 /usr/lib64/libm-2.17.so
2af553b06000-2af553b07000 r--p 00100000 08:03 148444 /usr/lib64/libm-2.17.so
2af553b07000-2af553b08000 rw-p 00101000 08:03 148444 /usr/lib64/libm-2.17.so
2af553b08000-2af553b1e000 r-xp 00000000 67:70864 144115273706872320 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libgcc_s.so.1
2af553b1e000-2af553d1d000 ---p 00016000 67:70864 144115273706872320 /lustre/shared/ucl/apps/gcc/4.9.2/lib64/libgcc_s.so.1
2af553d1d000-2af553d1e000 r--p 00015000 67:70864 144115273706872320 /lustre
/shared/ucl/apps/gcc/4.9.2/lib64/libgcc_s.so.1
2af553d1e000-2af553d1f000 rw-p 00016000 67:70864 144115273706872320 /lustre
/shared/ucl/apps/gcc/4.9.2/lib64/libgcc_s.so.1
2af553d1f000-2af553ee3000 r-xp 00000000 08:03 148170 /usr/li
b64/libc-2.17.so
2af553ee3000-2af5540e2000 ---p 001c4000 08:03 148170 /usr/li
b64/libc-2.17.so
2af5540e2000-2af5540e6000 r--p 001c3000 08:03 148170 /usr/li
b64/libc-2.17.so
2af5540e6000-2af5540e8000 rw-p 001c7000 08:03 148170 /usr/li
b64/libc-2.17.so
2af5540e8000-2af5540ed000 rw-p 00000000 00:00 0
2af5540ed000-2af554104000 r-xp 00000000 08:03 148564 /usr/li
b64/libpthread-2.17.so
2af554104000-2af554303000 ---p 00017000 08:03 148564 /usr/li
b64/libpthread-2.17.so
2af554303000-2af554304000 r--p 00016000 08:03 148564 /usr/li
b64/libpthread-2.17.so
2af554304000-2af554305000 rw-p 00017000 08:03 148564 /usr/lib64/libpthread-2.17.so
2af554305000-2af554309000 rw-p 00000000 00:00 0
2af558000000-2af558021000 rw-p 00000000 00:00 0
2af558021000-2af55c000000 ---p 00000000 00:00 0
7ffe2293b000-7ffe2295f000 rw-p 00000000 00:00 0 [stack]
7ffe22976000-7ffe22978000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
CatDCD 5.1
Reading indices from file 'indexfile'
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opening file 'all_combined.dcd' for writing.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Opened file 'MD_backbone_Wildtype_1.dcd' for reading.
------------------------------------------------------------------------------

Any ideas on what this error means or how I can fix it? I assume it has something to do with the issues in the merged file despite the fact that catdcd ends up running.

Best,
Christos

________________________________
From: Nick Bayhi <bayhi_at_uchicago.edu>
Sent: Sunday, July 2, 2023 1:32 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Concatenate DCD Files with Different Numbers of Atoms

I think you’d need to write the new dcd files out for just the backbone, but I haven’t done it myself now I’m not 100%.

For me, I have analyzed coarse grained simulations starting from various cryoEM structures of the same protein but with different N and C termini cutoffs; I had to save files all trimmed to the same length, in order to run PCA. That let me analyze them as if it was one long simulation, and I was able to color my plots differently for the frames that came from each mutant

On Sat, Jul 1, 2023 at 17:27 Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk<mailto:christos.dereschuk.20_at_ucl.ac.uk>> wrote:
Hi Nick,

If I create an index file for just the backbone/alpha carbon atoms and use the -index option in catdcd, would that work? Or would it still cause an error since the input dcd files themselves have different numbers of atoms? I am just curious if I need to rewrite the dcd files for each simulation just with the backbone or if I can just use the index option to get the combined backbone dcd file. Thanks for the help!

Best,
Christos
________________________________
From: Nick Bayhi <bayhi_at_uchicago.edu<mailto:bayhi_at_uchicago.edu>>
Sent: Sunday, July 2, 2023 1:13:31 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk<mailto:christos.dereschuk.20_at_ucl.ac.uk>>
Subject: Re: vmd-l: Concatenate DCD Files with Different Numbers of Atoms

⚠ Caution: External sender

Maybe try to save just the coordinates your your backbone/alpha carbons and running pca on that? Should give you the same usable information about how the whole protein moves, I’m not sure that pca would be reasonably interpretable down to the side chain

On Sat, Jul 1, 2023 at 17:09 Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk<mailto:christos.dereschuk.20_at_ucl.ac.uk>> wrote:
Hello,

I would like to concatenate some mutant simulations with wild type simulations to run PCA analysis. However, catdcd will not allow me to concatenate all the simulations into a single DCD file due to the different numbers of atoms between the wildtype and mutant as a result of the point mutations I introduced. How can I combine these files to run an accurate PCA? I have heard that it is necessary to combine all simulations into a single file to compare the wildtype and mutant as this ensures PC1, PC2, etc. are the same between the various simulations. I appreciate any advice!

Best,
Christos 

--
--
Nick Bayhi, (971) 219-7408
Wei-Jen Tang Lab<https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!-y-FFxsaGsAkm23bG_uuQBTFxz-L8oRUdKmlnI2kPEfey7vgecfZPQdtt0jADLrHdwWraop5bBgGsUEh6PFxEu81SsW9blU$ >
Biophysical Sciences Graduate Program
University of Chicago
--
--
Nick Bayhi, (971) 219-7408
Wei-Jen Tang Lab<https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!-y-FFxsaGsAkm23bG_uuQBTFxz-L8oRUdKmlnI2kPEfey7vgecfZPQdtt0jADLrHdwWraop5bBgGsUEh6PFxEu81SsW9blU$ >
Biophysical Sciences Graduate Program
University of Chicago