Hi
I suspect something wrong in your structure (mol2).
Have you checked if all valencies are satisfied?
Can you rename you atoms CA, C, OG, CB, H to something else,? Because this may clash with the atom names given to proteins. CA = alpha carbon; CB for beta carbon and so on...
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Nikolay N. Kuzmich [mailto:nnkuzmich.gmail.com]
Sent: Wednesday, February 22, 2017 8:50 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
Dear David, Elvis and other Amber users,
here's the prepin file:
0 0 2
This is a remark line
molecule.res
ADF INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
4 N33 NT M 3 2 1 1.540 111.208 -180.000 -0.868706
5 H H E 4 3 2 0.978 56.120 38.296 0.377435
6 CA CT M 4 3 2 1.415 69.875 -152.239 0.130662
7 CB CT 3 6 4 3 1.518 122.620 70.977 0.151056
8 OG OS S 7 6 4 1.393 106.138 -173.698 -0.431427
9 C21 CM B 8 7 6 1.342 127.171 -138.460 0.638042
10 C12 CT B 9 8 7 1.543 112.688 -179.098 -0.003511
11 C13 CT 3 10 9 8 1.541 104.831 -66.209 -0.091083
12 C14 CT 3 11 10 9 1.521 105.959 -103.625 -0.091083
13 C2 CT B 12 11 10 1.453 99.781 -35.209 0.026337
14 C1 CT 3 13 12 11 1.530 110.598 -68.820 0.051240
15 H1 H1 E 14 13 12 1.117 112.800 -83.624 0.058619
16 H2 H1 E 14 13 12 1.118 109.266 36.575 0.058619
17 N2 N B 14 13 12 1.449 100.153 151.822 -0.519683
18 C3 C B 17 14 13 1.332 109.343 -25.837 0.756817
19 N1 N E 18 17 14 1.346 98.851 -5.227 -0.379157
20 O1 O E 18 17 14 1.208 132.518 174.235 -0.583656
21 H4 H E 17 14 13 1.010 125.354 154.212 0.325375
22 H3 H1 E 13 12 11 1.117 116.464 164.820 0.085776
23 H141 HC E 12 11 10 1.090 109.032 -149.363 0.059131
24 H142 HC E 12 11 10 1.090 109.046 78.936 0.059131
25 H131 HC E 11 10 9 1.090 109.408 138.563 0.076553
26 H132 HC E 11 10 9 1.090 109.406 14.209 0.076553
27 H12 H1 E 10 9 8 1.090 107.877 48.596 0.104222
28 N22 DU S 9 8 7 1.348 124.496 0.318 -0.821214
29 HN22 H E 28 9 8 1.009 120.003 179.996 0.439025
30 HB3 H1 E 7 6 4 1.090 109.420 68.361 0.073478
31 HB2 H1 E 7 6 4 1.090 109.398 -55.775 0.073478
32 HA H1 E 6 4 3 1.090 101.229 -49.552 0.112421
33 C C M 6 4 3 1.553 102.644 -161.479 0.601661
34 O O E 33 6 4 1.395 113.429 48.890 -0.546111
LOOP
N1 C12
N1 C2
IMPROPER
C12 N22 C21 OG
N2 N1 C3 O1
C3 C2 N1 C12
CA +M C O
DONE
STOP
the main chain file:
*HEAD_NAME N33TAIL_NAME CMAIN_CHAIN CAOMIT_NAME HNOMIT_NAME O31OMIT_NAME H34PRE_HEAD_TYPE CPOST_TAIL_TYPE NCHARGE 0.0*
And the mol2 file, if it would be informative:
.<TRIPOS>MOLECULE
Structure3
34 35 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 CA 5.8790 -2.8150 -3.9420 C.3 1 ADF 0.0000
2 C 7.1110 -1.8710 -3.9890 C.2 1 ADF 0.0000
3 O 7.7100 -1.8030 -5.2470 O.2 1 ADF 0.0000
4 CB 5.2060 -2.8250 -2.5810 C.3 1 ADF 0.0000
5 OG 4.7380 -1.5300 -2.3710 O.3 1 ADF 0.0000
6 H 5.8210 -4.6280 -5.0640 H 1 ADF 0.0000
7 HA 5.1550 -2.4710 -4.6800 H 1 ADF 0.0000
8 HB3 5.9410 -3.0730 -1.8150 H 1 ADF 0.0000
9 HB2 4.3630 -3.5160 -2.5990 H 1 ADF 0.0000
10 C12 4.1510 0.5740 -1.3670 C.3 1 ADF 0.0000
11 C13 5.0640 1.3310 -2.3510 C.3 1 ADF 0.0000
12 C14 5.8970 2.2800 -1.5030 C.3 1 ADF 0.0000
13 C21 4.7900 -0.8240 -1.2310 C.2 1 ADF 0.0000
14 N22 5.3260 -1.2730 -0.0790 N.2 1 ADF 0.0000
15 H12 3.1770 0.4520 -1.8400 H 1 ADF 0.0000
16 H131 4.4510 1.9080 -3.0430 H 1 ADF 0.0000
17 H132 5.7220 0.6220 -2.8530 H 1 ADF 0.0000
18 H141 6.1320 3.1680 -2.0900 H 1 ADF 0.0000
19 H142 6.7080 1.7210 -1.0360 H 1 ADF 0.0000
20 HN22 5.3290 -0.6830 0.7400 H 1 ADF 0.0000
21 C1 3.7970 3.4800 -1.0910 C.3 1 ADF 0.0000
22 C2 4.9170 2.6290 -0.4880 C.3 1 ADF 0.0000
23 N1 4.0370 1.5970 -0.3900 N.am 1 ADF 0.0000
24 C3 2.9240 1.9120 0.2990 C.2 1 ADF 0.0000
25 O1 2.3420 1.2580 1.1320 O.2 1 ADF 0.0000
26 N2 2.7030 3.1230 -0.2110 N.am 1 ADF 0.0000
27 H1 4.0590 4.5640 -1.1460 H 1 ADF 0.0000
28 H2 3.5800 3.1230 -2.1280 H 1 ADF 0.0000
29 H3 5.3100 3.1180 0.4360 H 1 ADF 0.0000
30 H4 1.8980 3.7010 -0.0150 H 1 ADF 0.0000
31 O31 7.6198 -1.1465 -2.9513 O.3 1 ADF 0.0000
32 HN 7.2551 -4.1877 -4.5157 H 1 ADF 0.0000
33 N33 6.3662 -3.9906 -4.5609 N.3 1 ADF -0.3216
34 H34 8.3829 -0.6479 -3.2524 H 1 ADF 0.0000
.<TRIPOS>BOND
1 1 2 1
2 1 4 1
3 1 7 1
4 1 33 1
5 2 3 2
6 2 31 1
7 4 5 1
8 4 8 1
9 4 9 1
10 5 13 1
11 6 33 1
12 10 11 1
13 10 13 1
14 10 23 1
15 10 15 1
16 11 12 1
17 11 16 1
18 11 17 1
19 12 22 1
20 12 18 1
21 12 19 1
22 13 14 2
23 14 20 1
24 21 22 1
25 21 27 1
26 21 28 1
27 21 26 1
28 22 29 1
29 22 23 1
30 23 24 am BACKBONE|DICT|INTERRES
31 24 25 2
32 24 26 am BACKBONE|DICT|INTERRES
33 26 30 1
34 31 34 1
35 32 33 1
.<TRIPOS>SUBSTRUCTURE
1 ADF 1 GROUP 0 A **** 0 ROOT
Thank you,
Nick
Message: 32
Date: Tue, 21 Feb 2017 09:32:02 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170221143202.oaw4o3757hzyt65l.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Tue, Feb 21, 2017, Nikolay N. Kuzmich wrote:
>
> parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \
> $AMBERHOME/dat/leap/parm/parm10.dat
>
> And then I got message "Segmentation fault".
Can you post the prepin file you are using? We need this to try to reproduce the problem, which is a necessary first step in looking for a fix.
The term "segmentation fault" is just a generic error message, and doesn't provide any information.
...thx...dac
essage: 37
Date: Tue, 21 Feb 2017 16:21:23 +0000
From: "Elvis Martis" <elvis.martis.bcp.edu.in>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<PN1PR01MB0830FA5656289E7318CA3341A3510.PN1PR01MB0830.
INDPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Firstly, Segmentation fault is a general error message, can you post any log files.
Secondly, can tell us what are trying to simulate (little more details are
needed)
? ? Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
?at?Bombay College of Pharmacy
A??Kalina, Santacruz [E], Mumbai 400098, INDIA W?www.elvismartis.in
Skype.?adrian_elvis12
-----Original Message-----
From: Nikolay N. Kuzmich [mailto:nnkuzmich.gmail.com]
Sent: Tuesday, February 21, 2017 7:34 PM
To: amber.ambermd.org
Subject: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
Dear Amber users,
preparing necessary files for simulation of a protein with modified serine residue, I was checking the presense of parameters via parmchk2 application just as it is described in the "Simulating the Green Fluorescent Protein"
tutorial.
parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \ $AMBERHOME/dat/leap/parm/parm10.dat
The own generated prepin file was employed.
And then I got message "Segmentation fault".
I have found the similar report about this error in the archive via google but still hardly know what to do.
Is it a problem with my prepin file?
What should I pay attention to in it?
And what can be wrong there?
Thank you in advance,
Nick
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Received on Wed Feb 22 2017 - 08:30:02 PST
