date:20180601

Re: [gmx-users] Partial charges

2018-06-01 Thread Alex


This has got nothing to do with Gromacs.

A general comment: no, you should not neglect it. I am not sure what you 
mean by "QM," but the total charge of the system calculated by either 
DFT, or with Hartree-Fock, is _imposed_ and is not the result of 
calculations -- this sets up the sanity check for the density 
distribution. If you set up your QM calculations by demanding that the 
total charge is zero and the result is nonzero, you probably screwed 
something up with boundaries, basis sets, spin multiplicity, etc, etc, 
so the result is not trustworthy. Obtaining MD parameters from quantum 
chemistry is a whole field in itself.


Alex


On 6/1/2018 12:49 AM, rose rahmani wrote:

Hi,

I used QM for calculating atoms partial charges for ZnS nanotube but it has
totally -0.04 charge. I want to study the interaction of this nanotube with
some biomolecules by AMBER99SB force field.
Is it wrong to calculate these interaction in presence of -0.04 charge by
this force field? Should i neglect it?
Would you please help me or give me a suggestion?

Best regards


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Re: [gmx-users] Thread-MPI error in GROMACS-2018

2018-06-01 Thread Mark Abraham

Hi,

That error is a strong indicator of a code problem. There was a similar
report on here a few days ago about a tMPI error. Please do open an issue
at https://redmine.gromacs.org/ and attach those files above and your .tpr
so we can reproduce the issue and try to find and fix its cause.

Mark

On Fri, Jun 1, 2018 at 4:12 AM Siva Dasetty  wrote:

> Hello,
>
> I have come across an error that causes GROMACS (2018/2018.1) to crash. The
> message is:
>
> "tMPI error: Receive buffer size too small for transmission (in valid comm)
> Aborted"
>
> The error seems to only occur immediately following a LINCS or SETTLE
> warning. The error is reproducible across different systems. A simple
> example system is running an energy minimization on a box of 1000 rigid
> TIP4P/Ice water molecules generated with gmx solvate. When SETTLE is used
> as the constraint algorithm,  there are several SETTLE warnings in the
> early steps of the energy minimization, and GROMACS will crash with the
> above error message. If I replace SETTLE with LINCS, GROMACS crashes with
> the same error message following a LINCS warning. Other systems that have
> produced this error are -OH terminated self assembled monolayer surfaces
> (h-bonds constrained by LINCS), and mica surfaces (h-bonds constrained by
> LINCS).  Naturally, reducing -ntmpi to 1 eliminates the error for all
> cases.
>
> The problem does appear to be hardware dependent. Specifically, the tested
> node(s) on the cluster contains K20/K40 GPUs with Intel Xeon E5-2680v3
> processor (20/24 cores). I used GCC/5.4.0 and CUDA/8.0.44 compilers for
> installing GROMACS. An installation on my desktop machine with with very
> similar options does not have the thread MPI error.
>
> Example of procedure that causes error:
> # Node contains 24 cores and 2 K40 GPUs
> gmx solvate -cs tip4p -o box.gro -box 3.2 3.2 3.2 -maxsol 1000
> gmx grompp -f em.mdp -c box.gro -p tip4pice.top -o em
> export OMP_NUM_THREADS=6
> gmx mdrun -v -deffnm em -ntmpi 4 -ntomp 6 -pin on
>
> Attached are the relevant topology (tip4pice.top), mdp (em.mdp), and log
> (em.log) files.
>
> Thanks in advance for any ideas as to what might be causing this problem,
> Siva Dasetty
>
>  tip4pice.top
> <
> https://drive.google.com/a/g.clemson.edu/file/d/13e_rxBMNaizR1GvCVklc3IlQ1gcCTat_/view?usp=drive_web
> >
> 
>  em.mdp
> <
> https://drive.google.com/a/g.clemson.edu/file/d/1A1592_cB7jfwdBOcezkfsFnT4xPqksNB/view?usp=drive_web
> >
> 
>  em.log
> <
> https://drive.google.com/a/g.clemson.edu/file/d/15iU3364SwxpEx3popQf7elZ9_3p2r6v9/view?usp=drive_web
> >
> 
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[gmx-users] covar warning

2018-06-01 Thread venkat

Hi,
For PCA analysis  i tried to run covar tool for my task, i got following
warning 
"
WARNING: there are fewer frames in your trajectory than there are
 

degrees of freedom in your system. Only generating the first
 
400 out of 3564 eigenvectors and eigenvalues.
"
Why it generating 400  out of 3564 eigevectors,  How rectify this warning ?
kindly help .  (Command used : gmx_mpi covar -s prot_only-apo.pdb -f
PROTEIN.xtc -v eigenvect.trr -xpma covara.xpm)

Thank you
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[gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Wang, Yang

Hi,

I am dealing with a protein model using Gromacs. I got the PDB file from RCSB
bank (PID: 2slk) and I modified the residue name according to the rtp file.
Since the start terminal is ACE, I modified the end terminal from GLY/ALA to
CGLY/CALA. I ran it with pdb2gmx command but I still got the dangling bond
error. The error message showed that the error came from the last chain of NEM
residues. I guess it is probably still the name issue for the NEM cap. I am
wondering what residue name I should use for NEM.
Thanks a lot!

Command:
login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water tip3p
-ignh

Error:
~~
Select the Force Field:
>From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
..( Omit the other force fields)

Using the Amber03 force field in directory
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff

Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
Reading 2slk.pdb...
WARNING: all CONECT records are ignored
Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 16 chains and 0 blocks of water and 106 residues with 480 atoms

chain #res #atoms
1 'A' 7 30
2 'B' 7 30
3 'C' 7 30
4 'D' 7 30
5 'E' 7 30
6 'F' 7 30
7 'G' 7 30
8 'H' 7 30
9 'I' 7 30
10 'J' 7 30
11 'K' 7 30
12 'L' 7 30
13 'M' 7 30
14 'N' 7 30
15 'O' 7 30
16 'A' 1 30

All occupancies are one
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
Atomtype 68
Reading residue database... (amber03)
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb

..( Omit the chain 1-15)

Processing chain 16 'A' (30 atoms, 1 residues)
Identified residue NME8 as a starting terminus.
Identified residue NME8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/admin/rpms/BUILD/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1083

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues so
that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
~~

Best Regards,

Yang Wang

Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152...@utdallas.edu

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Re: [gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Mark Abraham

Hi,

Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
have to look at the contents of the pdb file to understand its contents.

Mark

On Fri, Jun 1, 2018, 16:33 Wang, Yang  wrote:

> Hi,
>
> I am dealing with a protein model using Gromacs. I got the PDB file from
> RCSB bank (PID: 2slk) and I modified the residue name according to the rtp
> file. Since the start terminal is ACE, I modified the end terminal from
> GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> dangling bond error.  The error message showed that the error came from the
> last chain of NEM residues. I guess it is probably still the name issue for
> the NEM cap. I am wondering what residue name I should use for NEM.
> Thanks a lot!
>
> Command:
> login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> tip3p -ignh
>
> Error:
>
> ~~
> Select the Force Field:
> From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
>  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> 1999-2012, 2003)
> ..( Omit the other force fields)
>
> 1
>
> Using the Amber03 force field in directory
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
>
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> Reading 2slk.pdb...
> WARNING: all CONECT records are ignored
> Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
>
>   chain  #res #atoms
>   1 'A' 7 30
>   2 'B' 7 30
>   3 'C' 7 30
>   4 'D' 7 30
>   5 'E' 7 30
>   6 'F' 7 30
>   7 'G' 7 30
>   8 'H' 7 30
>   9 'I' 7 30
>   10 'J' 7 30
>   11 'K' 7 30
>   12 'L' 7 30
>   13 'M' 7 30
>   14 'N' 7 30
>   15 'O' 7 30
>   16 'A' 1 30
>
> All occupancies are one
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
> Atomtype 68
> Reading residue database... (amber03)
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.hdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb
>
> ..( Omit the chain 1-15)
>
>
> Processing chain 16 'A' (30 atoms, 1 residues)
> Identified residue NME8 as a starting terminus.
> Identified residue NME8 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
> ---
> Program gmx pdb2gmx, VERSION 5.1.2
> Source code file:
> /admin/rpms/BUILD/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line: 1083
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends and the
> force field does not provide terminal entries or files. Fix your terminal
> residues so that they match the residue database (.rtp) entries, or provide
> terminal database entries (.tdb).
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> ~~
>
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. studen

Re: [gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Wang, Yang

Hi ,

I attached the PDB. It seems like cap ACE is listed in front of the main body 
of the chain but NME is separated from the chain and listed in the last part of 
the pbd file. And gromacs cannot tell that NME acrually belongs to each chain 
and thus separate all the NME to be a chain by itself. Right now I am moving 
the NME back to the tail part of each chain. I am not sure whether this is 
right way. Thanks a lot!



Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152...@utdallas.edu



From: Wang, Yang
Sent: Friday, June 1, 2018 10:13:01 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Dangling bond error using Amber force field.


Hi ,


I attached the PDB. It seems like cap ACE is listed in front of the main body 
of the chain but NME is separated from the chain and listed in the last part of 
the pbd file. And gromacs cannot tell that NME acrually belongs to each chain 
and thus separate all the NME to be a chain by itself. Right now I am moving 
the NME back to the tail part of each chain. I am not sure whether this is 
right way. Thanks a lot!


Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152...@utdallas.edu



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Friday, June 1, 2018 10:04:53 AM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Dangling bond error using Amber force field.

Hi,

Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
have to look at the contents of the pdb file to understand its contents.

Mark

On Fri, Jun 1, 2018, 16:33 Wang, Yang  wrote:

> Hi,
>
> I am dealing with a protein model using Gromacs. I got the PDB file from
> RCSB bank (PID: 2slk) and I modified the residue name according to the rtp
> file. Since the start terminal is ACE, I modified the end terminal from
> GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> dangling bond error.  The error message showed that the error came from the
> last chain of NEM residues. I guess it is probably still the name issue for
> the NEM cap. I am wondering what residue name I should use for NEM.
> Thanks a lot!
>
> Command:
> login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> tip3p -ignh
>
> Error:
>
> ~~
> Select the Force Field:
> From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
>  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> 1999-2012, 2003)
> ..( Omit the other force fields)
>
> 1
>
> Using the Amber03 force field in directory
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
>
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> Reading 2slk.pdb...
> WARNING: all CONECT records are ignored
> Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> They will be treated as separate chains unless you reorder your file.
> There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
>
>   chain  #res #atoms
>   1 'A' 7 30
>   2 'B' 7 30
>   3 'C' 7 30
>   4 'D' 7 30
>   5 'E' 7 30
>   6 'F' 7 30
>   7 'G' 7 30
>   8 'H' 7 30
>   9 'I' 7 30
>   10 'J' 7 30
>   11 'K' 7 30
>   12 'L' 7 30
>   13 'M' 7 30
>   14 'N' 7 30
>   15 'O' 7 30
>   16 'A' 1 30
>
> All occupancies are one
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
> Atomtype 68
> Reading residue database... (amber03)
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /opt/apps/intel

Re: [gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Mark Abraham

Hi,

The list can't accept attachments. It sounds like you need to set the chain
IDs for your terminal residues to match the IDs of their chains.

Mark

On Fri, Jun 1, 2018, 17:19 Wang, Yang  wrote:

> Hi ,
>
> I attached the PDB. It seems like cap ACE is listed in front of the main
> body of the chain but NME is separated from the chain and listed in the
> last part of the pbd file. And gromacs cannot tell that NME acrually
> belongs to each chain and thus separate all the NME to be a chain by
> itself. Right now I am moving the NME back to the tail part of each chain.
> I am not sure whether this is right way. Thanks a lot!
>
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152...@utdallas.edu
>
>
> 
> From: Wang, Yang
> Sent: Friday, June 1, 2018 10:13:01 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Dangling bond error using Amber force field.
>
>
> Hi ,
>
>
> I attached the PDB. It seems like cap ACE is listed in front of the main
> body of the chain but NME is separated from the chain and listed in the
> last part of the pbd file. And gromacs cannot tell that NME acrually
> belongs to each chain and thus separate all the NME to be a chain by
> itself. Right now I am moving the NME back to the tail part of each chain.
> I am not sure whether this is right way. Thanks a lot!
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152...@utdallas.edu
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Friday, June 1, 2018 10:04:53 AM
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Dangling bond error using Amber force field.
>
> Hi,
>
> Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
> have to look at the contents of the pdb file to understand its contents.
>
> Mark
>
> On Fri, Jun 1, 2018, 16:33 Wang, Yang  wrote:
>
> > Hi,
> >
> > I am dealing with a protein model using Gromacs. I got the PDB file from
> > RCSB bank (PID: 2slk) and I modified the residue name according to the
> rtp
> > file. Since the start terminal is ACE, I modified the end terminal from
> > GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> > dangling bond error.  The error message showed that the error came from
> the
> > last chain of NEM residues. I guess it is probably still the name issue
> for
> > the NEM cap. I am wondering what residue name I should use for NEM.
> > Thanks a lot!
> >
> > Command:
> > login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> > tip3p -ignh
> >
> > Error:
> >
> >
> ~~
> > Select the Force Field:
> > From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
> >  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> > 1999-2012, 2003)
> > ..( Omit the other force fields)
> >
> > 1
> >
> > Using the Amber03 force field in directory
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
> >
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> > Reading 2slk.pdb...
> > WARNING: all CONECT records are ignored
> > Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
> > Analyzing pdb file
> > Splitting chemical chains based on TER records or chain id changing.
> > WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> > They will be treated as separate chains unless you reorder your file.
> > There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
> >
> >   chain  #res #atoms
> >   1 'A' 7 30
> >   2 'B' 7 30
> >   3 'C' 7 30
> >   4 'D' 7 30
> >   5 'E' 7 30
> >   6 'F' 7 30
> >   7 'G' 7 30
> >   8 'H' 7 30
> >   9 'I' 7 30
> >   10 'J' 7 30
> >   11 'K' 7 30
> >   12 'L' 7 30
> >   13 'M' 7 30
> >   14 'N' 7 30
> >   15 'O' 7 30
> >   16 'A' 1 30
> >
> > All occupancies are one
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
> > Atomtype 68
> > Reading residue database...

Re: [gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Wang, Yang

Hi,


Thanks! Good to know. The PID is 2slk. And I use amber force field.


Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152...@utdallas.edu



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Friday, June 1, 2018 10:30:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Dangling bond error using Amber force field.

Hi,

The list can't accept attachments. It sounds like you need to set the chain
IDs for your terminal residues to match the IDs of their chains.

Mark

On Fri, Jun 1, 2018, 17:19 Wang, Yang  wrote:

> Hi ,
>
> I attached the PDB. It seems like cap ACE is listed in front of the main
> body of the chain but NME is separated from the chain and listed in the
> last part of the pbd file. And gromacs cannot tell that NME acrually
> belongs to each chain and thus separate all the NME to be a chain by
> itself. Right now I am moving the NME back to the tail part of each chain.
> I am not sure whether this is right way. Thanks a lot!
>
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152...@utdallas.edu
>
>
> 
> From: Wang, Yang
> Sent: Friday, June 1, 2018 10:13:01 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Dangling bond error using Amber force field.
>
>
> Hi ,
>
>
> I attached the PDB. It seems like cap ACE is listed in front of the main
> body of the chain but NME is separated from the chain and listed in the
> last part of the pbd file. And gromacs cannot tell that NME acrually
> belongs to each chain and thus separate all the NME to be a chain by
> itself. Right now I am moving the NME back to the tail part of each chain.
> I am not sure whether this is right way. Thanks a lot!
>
>
> Best Regards,
>
> Yang Wang
>
>
>
> Ph.D. student
>
> Department of Mechanical Engineering
>
> University of Texas at Dallas
>
> E-mail: yxw152...@utdallas.edu
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Friday, June 1, 2018 10:04:53 AM
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Dangling bond error using Amber force field.
>
> Hi,
>
> Chain 16 is clearly a problem (start and end residue is NME 8) but you'll
> have to look at the contents of the pdb file to understand its contents.
>
> Mark
>
> On Fri, Jun 1, 2018, 16:33 Wang, Yang  wrote:
>
> > Hi,
> >
> > I am dealing with a protein model using Gromacs. I got the PDB file from
> > RCSB bank (PID: 2slk) and I modified the residue name according to the
> rtp
> > file. Since the start terminal is ACE, I modified the end terminal from
> > GLY/ALA to CGLY/CALA.  I ran it with pdb2gmx command but I still got the
> > dangling bond error.  The error message showed that the error came from
> the
> > last chain of NEM residues. I guess it is probably still the name issue
> for
> > the NEM cap. I am wondering what residue name I should use for NEM.
> > Thanks a lot!
> >
> > Command:
> > login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water
> > tip3p -ignh
> >
> > Error:
> >
> >
> ~~
> > Select the Force Field:
> > From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
> >  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> > 1999-2012, 2003)
> > ..( Omit the other force fields)
> >
> > 1
> >
> > Using the Amber03 force field in directory
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff
> >
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
> > Opening force field file
> >
> /opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
> > Reading 2slk.pdb...
> > WARNING: all CONECT records are ignored
> > Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
> > Analyzing pdb file
> > Splitting chemical chains based on TER records or chain id changing.
> > WARNING: Chain identifier 'A' is used in two non-sequential blocks.
> > They will be treated as separate chains unless you reorder your file.
> > There are 16 chains and 0 blocks of water and 106 residues with 480 atoms
> >
> >   chain  #res #atoms
> >   1 'A' 7 30
> >   2 'B' 7 30
> >   3 'C' 7 30
> >   4 'D' 7 30
> >

Re: [gmx-users] Dangling bond error using Amber force field.

2018-06-01 Thread Wang, Yang

Hi Mark,


Got it! Thank you so much! I replaced the Terminal of each chain with the 
corresponding NME residues and now it recognized the NME as the end terminal. 
Now, it seems work. I have been struggling for days. Thanks a lot for the help!


Best Regards,

Yang Wang



Ph.D. student

Department of Mechanical Engineering

University of Texas at Dallas

E-mail: yxw152...@utdallas.edu



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Wang, Yang 

Sent: Friday, June 1, 2018 9:32:38 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Dangling bond error using Amber force field.

Hi,

I am dealing with a protein model using Gromacs. I got the PDB file from RCSB 
bank (PID: 2slk) and I modified the residue name according to the rtp file. 
Since the start terminal is ACE, I modified the end terminal from GLY/ALA to 
CGLY/CALA.  I ran it with pdb2gmx command but I still got the dangling bond 
error.  The error message showed that the error came from the last chain of NEM 
residues. I guess it is probably still the name issue for the NEM cap. I am 
wondering what residue name I should use for NEM.
Thanks a lot!

Command:
login2.ls5(1076)$ gmx pdb2gmx -f 2slk.pdb -o 2slk_processed.gro -water tip3p 
-ignh

Error:
~~
Select the Force Field:
>From '/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
..( Omit the other force fields)

1

Using the Amber03 force field in directory 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff

Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.r2b
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.r2b
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.r2b
Reading 2slk.pdb...
WARNING: all CONECT records are ignored
Read '2 FIBROIN PEPTIDES. I. SHEETS OF POLY(ALA-GLY) CHAINS', 480 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 16 chains and 0 blocks of water and 106 residues with 480 atoms

  chain  #res #atoms
  1 'A' 7 30
  2 'B' 7 30
  3 'C' 7 30
  4 'D' 7 30
  5 'E' 7 30
  6 'F' 7 30
  7 'G' 7 30
  8 'H' 7 30
  9 'I' 7 30
  10 'J' 7 30
  11 'K' 7 30
  12 'L' 7 30
  13 'M' 7 30
  14 'N' 7 30
  15 'O' 7 30
  16 'A' 1 30

All occupancies are one
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/atomtypes.atp
Atomtype 68
Reading residue database... (amber03)
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file 
/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top/amber03.ff/aminoacids.c.tdb

..( Omit the chain 1-15)


Processing chain 16 'A' (30 atoms, 1 residues)
Identified residue NME8 as a starting terminus.
Identified residue NME8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/admin/rpms/BUILD/gromacs-5.1.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 
1083

Fatal error:
There is a dangling bond at at least one of the terminal ends and the force 
field does not provide terminal entries or files. Fix your terminal residues so 
that they match the residue database (.rtp) entries, or provide terminal 
database entries (.tdb).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Doc

Re: [gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

2018-06-01 Thread Thomas Piggot


Hi Seyed,

You might want to take a look at the modified version of g_order (gmx 
order) provided as part of the SI of one of my papers:


https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00643

This code should be able to calculate order parameters at defined radial 
distances around a central object. You can find more details about the 
radial calculation in the work (and SI) of the below paper from Reid Van 
Lehn, who provided most of the modifications to the g_order program 
including this radial calculation:


https://pubs.acs.org/doi/abs/10.1021/jp506239p

I wasn't really interested in this part of the code for what I was doing 
and so you should check for yourself that it is working correctly.


Cheers

Tom

On 31/05/18 11:08, Mark Abraham wrote:

Hi,

Analysis based on so-called "dynamic selections" need to be done in this
way - form the selection and then compute based upon it. That can be tricky
if the selection is constructed in such a way that it does not always have
the same number of molecules and/or particles. Generally one needs to
construct the atomic indices (ie. in an index group in an index file) and
use a tool that matches the selection to a frame, but few of the GROMACS
tools are (yet) capable of this.

I don't know how order parameters are calculated in order to comment any
further.

Mark

On Thu, May 31, 2018 at 11:48 AM Seyed Mojtaba Rezaei Sani <
s.m.rezaeis...@gmail.com> wrote:


Hi Mark,

Thank you for your answer. Actually, to define the shell size I use the
distance between the phosphorus of neighboring lipids and the center of
mass of the drug. I use gmx select to find phosphorus atoms accommodated in
the shell and then manually find the corresponding acyl chains in all four
regions (which is not an easy and fast method). Moreover, I am conducting
an umbrella sampling simulation with nearly 40 windows. In each window the
drug is allowed to move freely in the x-y plane and consequently the
locations of regions change spatially which makes the calculation
extraordinary difficult for me. Do have any more intelligent idea to do
this?

On Thu, May 31, 2018 at 12:08 PM, Mark Abraham 
wrote:


Hi,

gmx select is the tool for making complicated selections. See its
documentation.

Mark

On Wed, May 30, 2018 at 2:57 PM Seyed Mojtaba Rezaei Sani <
s.m.rezaeis...@gmail.com> wrote:


Dear all,

I am trying to calculate the order parameter of lipid acyl chains in a
bilayer surrounding a drug molecule using Gromacs. To do this, I

defined

four regions in the bilayer: two local regions within a considered

shell

in

the x-y plane around the drug (one for the leaflet containing the drug

and

the other for the opposite one) and two global regions beyond the

shell.

My problem is that how to find lipid molecules which are located in the
local shell in order to make an index group of their carbon chains for
calculation of order parameter. Is there any Gromacs' tool for such
calculation?

Best regards,


--
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310 <+98%2021%202310> <+98%2021%202310>  (3069)
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Support/Mailing_Lists/GMX-Users_List before posting!

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send a mail to gmx-users-requ...@gromacs.org.




--
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310 <+98%2021%202310>  (3069)
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send a mail to gmx-users-requ...@gromacs.org.



--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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[gmx-users] Water in hydrophobic core of POPC lipid bilayer

2018-06-01 Thread Smith, Iris

Hello,

I have successfully completed the KALP-15 in DPPC membrane tutorial recently 
and have since moved on to setting up my own protein-membrane system.

For my system I am using POPC lipid parameters with GROMOS 53a6 ff obtained 
from the Lipidbook (2010 Poger and Mark version). After solvating my system, 
water flooded the hydrophobic core within the POPC lipid bilayer.  I have 
modified the vdw for the carbon atoms by increasing from 0.15 to 0.375. 
However, I don’t want to arbitrarily increase the vdw again without possibly 
causing artificial voids around my protein.

Can someone offer suggestions? Thank you for your help.

Best,
Iris





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[gmx-users] Cavity in the system after NVT equilibration

2018-06-01 Thread Alex

Dear all,
I have a system containing 4000 water molecules+700 of molecule A + 300 of
molecule B. After minimization, the system undergoes a 2ns NVT equalization
at 298.15 K which gives a big cavity in the system at the end, whereas the
cavity does not show up at 650 K equlibration. But what I need is the
system at 298.15 K. So, I tried to rampe down the temperature from fully
equilibrated system at 650 to 298.15 by the step of 35 K (in total 10 ns)
hoping to solve the problem by cooling down the system from the temperature
at which the system is normal to the desired temperature, but at the end
the cavity appears  unfortunately.
So, I wonder how I should equilibrate the system in order to avoid having
the cavity?
Thank you,
Alex
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Re: [gmx-users] Cavity in the system after NVT equilibration

2018-06-01 Thread Alex

Equilibration under NVT is a very bizarre approach, I am not even going 
to ask why you're doing this.


I am known for perverse use of Gromacs, but please follow EM > NPT 
equilibration (Berendsen thermostat, etc) > production.


The fact that you don't see the cavity at high temperature is that you 
have overheated gas under high pressure. The fact that annealing it down 
brings back the cavity means that the physics works and everyone should 
rejoice.


Alex


On 6/1/2018 10:21 PM, Alex wrote:

Dear all,
I have a system containing 4000 water molecules+700 of molecule A + 300 of
molecule B. After minimization, the system undergoes a 2ns NVT equalization
at 298.15 K which gives a big cavity in the system at the end, whereas the
cavity does not show up at 650 K equlibration. But what I need is the
system at 298.15 K. So, I tried to rampe down the temperature from fully
equilibrated system at 650 to 298.15 by the step of 35 K (in total 10 ns)
hoping to solve the problem by cooling down the system from the temperature
at which the system is normal to the desired temperature, but at the end
the cavity appears  unfortunately.
So, I wonder how I should equilibrate the system in order to avoid having
the cavity?
Thank you,
Alex


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Re: [gmx-users] Cavity in the system after NVT equilibration

2018-06-01 Thread Shreyas Kaptan

The cavity, which is due to negative pressure in the system, might imply
one of the two things:

The Box is too big for the system or that the MD simulation implodes the
system somehow. I have seen issues like these when the system is not well
minimized and has some obvious artefacts like "broken" bonds or missing
atoms in the structure and in topology.

But if it is none of the above, I would try a smaller timestep if possible.
Maybe it is a bad clash that somehow generates a negative pressure in the
system (although I do not profess to know how).

On Sat, Jun 2, 2018 at 6:28 AM Alex  wrote:

> Equilibration under NVT is a very bizarre approach, I am not even going
> to ask why you're doing this.
>
> I am known for perverse use of Gromacs, but please follow EM > NPT
> equilibration (Berendsen thermostat, etc) > production.
>
> The fact that you don't see the cavity at high temperature is that you
> have overheated gas under high pressure. The fact that annealing it down
> brings back the cavity means that the physics works and everyone should
> rejoice.
>
> Alex
>
>
> On 6/1/2018 10:21 PM, Alex wrote:
> > Dear all,
> > I have a system containing 4000 water molecules+700 of molecule A + 300
> of
> > molecule B. After minimization, the system undergoes a 2ns NVT
> equalization
> > at 298.15 K which gives a big cavity in the system at the end, whereas
> the
> > cavity does not show up at 650 K equlibration. But what I need is the
> > system at 298.15 K. So, I tried to rampe down the temperature from fully
> > equilibrated system at 650 to 298.15 by the step of 35 K (in total 10 ns)
> > hoping to solve the problem by cooling down the system from the
> temperature
> > at which the system is normal to the desired temperature, but at the end
> > the cavity appears  unfortunately.
> > So, I wonder how I should equilibrate the system in order to avoid having
> > the cavity?
> > Thank you,
> > Alex
>
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Shreyas Sanjay Kaptan
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