DDGmichigan commented 5 years ago

I am using spam to calculate free energies for a mixed solvent MD simulation (protein is ABL kinase) My input file is as follows: parm /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_2pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_2pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_3pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_3pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_4pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_4pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_5pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_5pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_6pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_6pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_7pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_7pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_8pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_8pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/New4H_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_10pmemdcuda/New4G_production.1.crd 1 50 1 trajin /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_10pmemdcuda/New4H_production.1.crd 1 50 1

Center and process image

center :1-286 mass origin

image origin familiar com :1-286

# autoimage

Align trajectory to reference structure by minimizing RMSD

reference /users/dicksmit/gphani/unsabi/users2/gphani/3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/setup_solvbox/3kfa_layer_ACN_H2O_5-95vv.pdb strip :Cl-,Na+ rms reference mass out 3kfa_ACN_15-20ns_md_CA_rmsd.txt :1-286@CA spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -30.3 dhbulk -22.2 info info.txt summary spam_summary.out out spam_energies.out

Error I get is:

Read 1000 frames and processed 1000 frames. TIME: Avg. throughput= 16.8114 frames / second.

ACTION OUTPUT: SPAM timing data: TIME: Residue c.o.m. calc: 0.0058 s ( 0.02%) TIME: Peak assignment : 0.0196 s ( 0.07%) TIME: Occupancy calc. : 0.0013 s ( 0.00%) TIME: Energy calc : 27.4013 s ( 99.89%) TIME: Residue reordering : 0.0040 s ( 0.01%) TIME: SPAM Action Total: 27.4324 s terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

DDGmichigan commented 4 years ago

@drroe Will try it today and update you of the results obtained. Thanks!

DDGmichigan commented 4 years ago

Hello Dan, Best wishes for having a new member addition to your family. Congrats in advance!

I know you may be too busy, I just wanted to ask do I need to install the latest Github version of cpptraj to see the changes #838 merged ? I think I am a little confused. Thanks Debarati

From: Daniel R. Roemailto:notifications@github.com Sent: 21 August 2020 16:34 To: Amber-MD/cpptrajmailto:cpptraj@noreply.github.com Cc: DDGmichiganmailto:debarati_dasgupta@hotmail.com; Mentionmailto:mention@noreply.github.com Subject: Re: [Amber-MD/cpptraj] SPAM throws error of 'std::bad_alloc' (#710)

Once #838https://github.com/Amber-MD/cpptraj/pull/838 passes I will merge it and you should be good to go.

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drroe commented 4 years ago

I just wanted to ask do I need to install the latest Github version of cpptraj to see the changes #838 merged ?

Yes, you need the latest GitHub version.

DDGmichigan commented 4 years ago

Thank you! Debarati

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From: Daniel R. Roemailto:notifications@github.com Sent: 26 August 2020 14:10 To: Amber-MD/cpptrajmailto:cpptraj@noreply.github.com Cc: DDGmichiganmailto:debarati_dasgupta@hotmail.com; Mentionmailto:mention@noreply.github.com Subject: Re: [Amber-MD/cpptraj] SPAM throws error of 'std::bad_alloc' (#710)

I just wanted to ask do I need to install the latest Github version of cpptraj to see the changes #838https://github.com/Amber-MD/cpptraj/pull/838 merged ?

Yes, you need the latest GitHub version.

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DDGmichigan commented 4 years ago

Hello Daniel. So I used the latest Github version of cpptraj : CPPTRAJ: Trajectory Analysis. V4.29.7 (GitHub)

This is my input file

parm /users/debarati/CHK_Kinase/ACN/setup_solvbox/1zys_layer_ACN_H2O_5-95vv.prmtop

trajin /users/debarati/CHK_Kinase/ACN/1zys_md_1pmemdcuda/New4A_production.1.crd 1 1250 1

##Align trajectory to reference structure by minimizing RMSD
solvent  :C3N,WAT
autoimage
strip :Na+
reference /users/debarati/CHK_Kinase/ACN/setup_solvbox/1zys_layer_ACN_H2O_5-95vv.pdb
rms reference mass out 3rcj_ACN_md_RMSD.txt :2-272@CA,C,N

volmap :C3N centermask :C3N@C2  buffer 4.0 peakfile ACN_peak.xyz 0.5 0.5 0.5 peakcut 0.04
run
spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -28 dhbulk -22 info info.txt summary spam_summary.out out spam_energies.out
run

It gives an output containing 25 peaks in a .xyz file called ACN_peak.xyz However, the spam_summary.out file has results on 17 peaks only... Why is it not printing out free energies associated with all 25 peak densities? Thanks

spam_summary.zip

swails commented 4 years ago

It gives an output containing 25 peaks in a .xyz file called ACN_peak.xyz However, the spam_summary.out file has results on 17 peaks only...

Are you sure there is a water molecule near the peak in enough frames to compute a free energy? My guess is that some peaks had such low "occupancy" that it couldn't effectively compute a free energy.

DDGmichigan commented 4 years ago

@swails Hello, its actually the acetonitrile peaks that I want to find and compute free energy for. So in my spam input file I have stated specifically solv C3N.. I am thinking is it something to do with the centermask command, should I centermask my C3N molecules? Thanks

DDGmichigan commented 4 years ago

@swails @drroe This is my volmap output (peak.xyz file) 25

C -15.83458426 -3.48751096 -24.02496346 0.18208355 C -15.33458426 -3.48751096 -5.02496346 0.07215087 C -13.33458426 -3.98751096 -7.52496346 0.08481847 C -7.83458426 1.51248904 -26.52496346 0.18277970 C -6.33458426 2.01248904 17.47503654 0.04097491 C -5.83458426 0.01248904 7.47503654 0.07941896 C -3.83458426 -2.48751096 5.97503654 0.09713764 C -2.83458426 -6.48751096 2.97503654 0.05333410 C 0.16541574 -1.98751096 4.47503654 0.16950871 C 2.16541574 -4.98751096 -3.02496346 0.07789360 C 2.16541574 -2.48751096 -25.52496346 0.17011112 C 3.66541574 9.01248904 -18.02496346 0.10714848 C 4.16541574 -13.98751096 9.47503654 0.05101398 C 5.16541574 6.01248904 16.47503654 0.06606977 C 6.66541574 -6.98751096 17.47503654 0.11398371 C 7.66541574 6.51248904 -22.52496346 0.06568318 C 8.66541574 1.51248904 15.97503654 0.10052010 C 9.66541574 15.51248904 -6.02496346 0.04698595 C 13.16541574 -4.98751096 -11.02496346 0.06496109 C 15.66541574 0.01248904 -3.52496346 0.07062216 C 16.66541574 2.01248904 6.47503654 0.04080936 C 17.16541574 -3.98751096 6.47503654 0.04096473 C 17.66541574 2.01248904 -11.52496346 0.04668125 C 18.66541574 -3.48751096 -0.52496346 0.04460616 C 19.16541574 3.01248904 -5.52496346 0.05725256

This has 25 peaks.. Now the spam_summary.out file has

Peak SPAM_00006[DG] SPAM_00006[DH] SPAM_00006[-TDS]

6.000 4.7246 3.1735 1.5512 7.000 0.3849 3.4466 -3.0617 9.000 4.2782 4.2530 0.0252 10.000 12.6775 7.8090 4.8685 12.000 7.1990 3.1199 4.0791 13.000 9.0568 5.4626 3.5943 14.000 3.4549 4.6195 -1.1646 15.000 -1.4712 2.2184 -3.6896 16.000 2.4221 6.1930 -3.7710 17.000 -0.0194 2.3838 -2.4032 18.000 -0.8356 3.4499 -4.2855 19.000 -3.9548 4.5259 -8.4807 20.000 10.6808 5.5195 5.1613 21.000 1.8647 3.1820 -1.3174 23.000 4.0945 2.1231 1.9713 24.000 -6.9405 1.8308 -8.7713 25.000 -1.0086 2.2322 -3.2408

DDGmichigan commented 4 years ago

The first 4 peaks in the peak.xyz file have the highest occupancy, then why is the energy not being printed out? @swails

drroe commented 4 years ago

volmap :C3N centermask :C3N@C2 buffer 4.0 peakfile ACN_peak.xyz 0.5 0.5 0.5 peakcut 0.04 run spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -28 dhbulk -22 info info.txt summary spam_summary.out out spam_energies.out

Why are you using a different peaks file in the spam command than you are generating with volmap?

DDGmichigan commented 4 years ago

That was a typo on my part (Sorry), but even after fixing that I get 31 peaks in my .xyz file (generated with volmap) and get only 20 peak energies in my spam_summary.out file... Debarati

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From: Daniel R. Roemailto:notifications@github.com Sent: 04 September 2020 13:30 To: Amber-MD/cpptrajmailto:cpptraj@noreply.github.com Cc: DDGmichiganmailto:debarati_dasgupta@hotmail.com; Mentionmailto:mention@noreply.github.com Subject: Re: [Amber-MD/cpptraj] SPAM throws error of 'std::bad_alloc' (#710)

volmap :C3N centermask :C3N@C2 buffer 4.0 peakfile ACN_peak.xyz 0.5 0.5 0.5 peakcut 0.04 run spam 3kfa_ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -28 dhbulk -22 info info.txt summary spam_summary.out out spam_energies.out

Why are you using a different peaks file in the spam command than you are generating with volmap?

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DDGmichigan commented 4 years ago

Hello Daniel, I need some help with the volmap command: So basically I have 4 similar input files and the difference lies in how I grid the solvent density using volmap: Case 1 : volmap :C3N centermask :C3N@C2 buffer 4.0 peakfile ACN_peak.xyz 0.5 0.5 0.5 peakcut 0.04 Case 2 : volmap :C3N centermask :C3N@C2 buffer 4.0 peakfile ACN_peak.xyz 200 200 200 0.5 0.5 0.5 peakcut 0.04 Case 3: volmap :C3N centermask ^1 buffer 5.0 peakfile 3kfa_ACN_peak.xyz dx 1.0 Case 4: volmap C3N_test.xplor 0.5 0.5 0.5 :C3N name GRID size 200,200,200 center origin peakcut 0.004 peakfile ACN_peak.xyz

So what is the difference in terms of the volmap functionality if I use case1 vs case2 vs others.... I think I am not able to use the correct command and its the reason why I get different peaks each time and wrong energies. Could you throw some light.. Thanks

Amber-MD / cpptraj

SPAM throws error of 'std::bad_alloc' #710

Center and process image

center :1-286 mass origin

image origin familiar com :1-286

Align trajectory to reference structure by minimizing RMSD

Peak SPAM_00006[DG] SPAM_00006[DH] SPAM_00006[-TDS]